Contacts of the helix formed by residues 31 - 53 (chain G) in PDB entry 5E94
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 31 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ASP* 3.6 4.7 - - - -
51B TYR* 3.0 30.3 + - - -
53B SER* 3.4 20.4 - - - -
54B TYR* 4.0 9.1 + - - -
57B SER* 4.9 2.7 - - - -
29G THR 5.3 1.7 + - - -
30G VAL* 1.3 77.9 - - - +
32G LEU* 1.3 63.7 + - - +
33G TRP 3.6 0.2 + - - -
34G GLU* 3.0 24.6 + - - +
35G THR* 3.1 27.0 + - - -
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Residues in contact with LEU 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B THR* 3.6 23.8 - - + +
33B TYR* 4.1 2.9 - - + -
34B ASP* 2.9 20.3 + - - +
54B TYR* 3.8 6.4 - - + -
99B ALA 3.6 24.2 - - - +
100B THR* 3.7 22.4 - - - -
101B ALA* 3.9 7.9 - - + +
103B PHE* 3.9 26.7 - - + -
108B TYR* 4.0 8.5 - - + -
31G SER* 1.3 71.7 - - - +
33G TRP* 1.3 58.5 + - - +
35G THR* 3.3 6.3 + - + -
36G VAL* 3.0 26.5 + - - +
141G LEU* 4.0 18.8 - - + -
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Residues in contact with TRP 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLY 3.8 10.5 - - - -
92A ASN 3.7 23.1 - - - -
93A THR* 4.4 0.2 - - - -
94A LEU* 3.5 41.7 - - + +
96A PHE* 3.8 25.6 - + - -
34B ASP* 2.9 16.1 + - - +
51B TYR* 3.7 28.0 - + + +
59B ASN* 5.3 0.7 - - - -
108B TYR* 3.6 41.7 - + + +
32G LEU* 1.3 77.4 - - - +
34G GLU* 1.3 63.8 + - - +
36G VAL* 3.2 6.4 + - + +
37G GLN* 3.0 58.3 + - + +
40G ARG* 3.8 15.9 - - - -
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Residues in contact with GLU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 5.4 0.2 - - - +
29G THR* 2.7 44.2 + - - +
30G VAL* 4.8 0.4 - - - -
31G SER* 3.0 25.1 + - - +
33G TRP* 1.3 77.0 - - + +
35G THR* 1.3 63.2 + - - +
37G GLN* 3.3 16.6 + - - +
38G LYS* 3.0 53.8 + - + +
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Residues in contact with THR 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B TYR* 5.0 2.1 + - - -
103B PHE* 4.0 22.7 - - + -
30G VAL* 6.0 0.7 - - - +
31G SER 3.1 14.3 + - - -
32G LEU* 3.6 10.7 - - + -
34G GLU* 1.3 77.9 - - - +
36G VAL* 1.3 58.5 + - - +
38G LYS* 3.2 10.2 + - - +
39G TRP* 2.8 27.2 + - - +
88G TYR* 3.6 25.3 + - + +
90G PRO* 3.8 29.9 - - + +
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Residues in contact with VAL 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ALA* 3.4 32.1 - - + -
102B SER 5.5 0.2 - - - +
103B PHE* 4.1 18.8 - - + -
106B GLY* 3.4 29.6 - - - +
107B SER 4.7 0.4 - - - +
108B TYR* 4.3 6.7 - - + -
32G LEU* 3.0 17.0 + - + +
33G TRP* 3.5 18.6 - - + +
35G THR* 1.3 77.4 - - - +
37G GLN* 1.3 57.8 + - - +
39G TRP* 3.1 3.8 + - - +
40G ARG* 2.9 44.1 + - - +
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Residues in contact with GLN 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASN 5.6 0.8 + - - +
93A THR* 5.8 1.0 - - - +
94A LEU* 5.2 3.8 - - - +
33G TRP* 3.0 65.4 + - + +
34G GLU* 3.3 17.9 + - - +
36G VAL* 1.3 76.7 - - - +
38G LYS* 1.3 63.5 + - + +
40G ARG* 3.3 14.6 + - - +
41G GLU* 3.0 22.5 + - - +
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Residues in contact with LYS 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G GLU* 3.0 49.2 + - + +
35G THR* 3.2 6.7 + - - +
37G GLN* 1.3 75.7 - - + +
39G TRP* 1.3 58.3 + - - +
41G GLU* 3.3 2.5 + - - -
42G TYR* 2.8 28.8 + - - +
87G TRP* 3.6 31.9 + - + +
88G TYR* 3.5 34.3 - - + +
89G LEU 5.8 1.4 + - - -
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Residues in contact with TRP 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE* 3.3 49.3 + + + +
104B TYR 3.7 4.5 - - - -
105B ASP 3.5 4.9 - - - -
106B GLY* 3.3 38.6 - - - -
35G THR 2.8 16.7 + - - +
36G VAL* 3.5 6.7 - - - +
38G LYS* 1.3 71.8 - - - +
40G ARG* 1.3 59.6 + - + +
42G TYR* 3.1 3.5 + - - +
43G ARG* 2.8 72.0 + - - -
66G PHE* 3.9 16.5 - + - -
68G GLU* 2.9 34.5 + - - -
88G TYR* 3.6 39.9 - + + +
142G LEU* 5.2 0.2 - - + -
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Residues in contact with ARG 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 3.3 43.8 - - - +
91A GLY 3.0 22.0 + - - -
92A ASN* 3.1 28.7 + - - +
106B GLY 2.8 27.9 + - - +
107B SER* 4.2 3.0 - - - +
108B TYR 4.3 2.2 - - - +
33G TRP* 3.8 15.5 - - - -
36G VAL* 2.9 23.9 + - - +
37G GLN* 3.5 14.8 - - - +
38G LYS 3.3 0.2 - - - -
39G TRP* 1.3 92.1 - - + +
41G GLU* 1.3 58.7 + - - +
43G ARG* 3.3 6.8 + - - +
44G ARG* 3.0 27.5 + - - +
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Residues in contact with GLU 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G GLN 3.0 16.8 + - - +
38G LYS* 3.7 5.6 - - - +
39G TRP 3.2 0.2 - - - -
40G ARG* 1.3 72.3 - - - +
42G TYR* 1.3 68.4 + - - +
44G ARG* 2.7 46.7 + - - +
45G GLN* 2.9 52.7 + - - +
87G TRP* 3.9 11.9 - - + -
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Residues in contact with TYR 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G LYS 2.8 14.0 + - - +
39G TRP 3.3 8.1 - - - +
41G GLU* 1.3 77.2 - - - +
43G ARG* 1.3 56.3 + - - +
45G GLN* 3.7 3.9 - - - +
46G CYS* 2.9 25.3 + - + +
66G PHE* 3.7 32.1 - + - -
69G TYR 4.0 5.6 - - - -
70G ALA* 3.5 9.7 - - - +
71G CYS* 3.0 35.3 + - + +
83G VAL* 4.6 6.9 - - - +
84G SER 5.1 0.5 + - - -
86G PRO* 4.0 19.8 - - + +
87G TRP* 3.2 46.5 - + + +
88G TYR* 3.6 24.7 - + + -
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Residues in contact with ARG 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 3.3 25.9 + - - -
50A TYR* 4.8 8.7 + - - -
104B TYR 4.1 3.4 + - - -
105B ASP* 3.4 18.2 + - - +
39G TRP* 2.8 49.3 + - + +
40G ARG* 3.6 11.1 + - - +
41G GLU 3.2 0.2 - - - -
42G TYR* 1.3 73.6 - - - +
44G ARG* 1.3 57.5 + - - +
46G CYS* 3.2 4.3 + - - +
47G GLN* 2.8 56.1 + - + +
66G PHE* 3.6 34.3 - - + -
68G GLU* 5.0 1.3 + - - -
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Residues in contact with ARG 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G ARG 3.0 14.2 + - - +
41G GLU* 2.7 42.3 + - - +
43G ARG* 1.3 75.7 - - - +
45G GLN* 1.3 74.1 + - - +
47G GLN* 3.3 15.3 + - - +
48G ARG* 3.1 53.9 + - - +
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Residues in contact with GLN 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G GLU* 2.9 48.8 + - - +
42G TYR* 3.7 3.8 - - + +
44G ARG* 1.3 83.0 - - - +
46G CYS* 1.3 65.7 + - - +
48G ARG* 3.2 10.4 + - - +
49G SER* 3.0 24.2 + - - -
87G TRP* 3.6 29.7 + - - -
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Residues in contact with CYS 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G TYR* 2.9 19.6 + - + +
43G ARG 3.6 4.9 - - - +
45G GLN* 1.3 76.1 - - - +
47G GLN* 1.3 58.4 + - + +
49G SER* 3.0 8.3 + - - -
50G LEU* 2.8 36.3 + - - +
66G PHE* 3.5 37.7 - - + -
71G CYS* 2.1 54.3 - - + -
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Residues in contact with GLN 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G ARG* 2.8 49.2 + - + +
44G ARG* 3.6 18.0 - - - +
45G GLN 3.3 0.2 - - - -
46G CYS* 1.3 77.2 - - + +
48G ARG* 1.3 63.8 + - - +
50G LEU* 3.4 16.1 + - + +
51G THR* 3.1 28.0 + - - +
66G PHE* 5.8 2.9 - - + -
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Residues in contact with ARG 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G ARG* 3.1 38.2 + - - +
45G GLN* 3.2 12.1 + - - +
47G GLN* 1.3 76.3 - - - +
49G SER* 1.3 52.8 + - - +
51G THR* 3.2 3.6 + - - -
52G GLU* 2.8 78.2 + - - +
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Residues in contact with SER 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G GLN 3.0 13.5 + - - -
46G CYS* 3.3 10.9 - - - -
48G ARG* 1.3 75.0 - - - +
50G LEU* 1.3 63.9 + - - +
52G GLU* 5.1 0.7 - - - -
53G ASP* 3.0 51.4 + - - +
64G ARG* 3.7 1.1 + - - -
71G CYS* 4.7 8.7 - - - -
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Residues in contact with LEU 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G CYS* 2.8 37.3 + - - +
47G GLN* 3.7 18.2 - - + +
48G ARG 3.3 0.2 - - - -
49G SER* 1.3 72.1 - - - +
51G THR* 1.3 59.6 + - - +
64G ARG* 2.7 50.7 + - + +
65G THR* 3.6 35.2 - - - +
66G PHE* 4.2 14.6 - - + +
71G CYS* 4.6 2.5 - - - -
72G TRP 4.4 2.7 - - - +
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Residues in contact with THR 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G GLN* 3.1 16.5 + - - +
48G ARG* 3.9 3.1 - - - -
50G LEU* 1.3 81.5 - - - +
52G GLU* 1.3 68.7 + - + +
53G ASP 4.6 2.6 - - - +
64G ARG* 4.7 0.7 + - - -
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Residues in contact with GLU 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ARG* 2.8 64.6 + - + +
49G SER* 5.1 0.9 - - - -
51G THR* 1.3 83.2 - - + +
53G ASP* 1.3 66.6 + - - +
54G PRO* 3.6 4.2 - - - +
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Residues in contact with ASP 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G SER* 3.0 42.6 + - - +
51G THR 3.7 2.5 - - - +
52G GLU* 1.3 80.3 - - - +
54G PRO* 1.3 75.6 - - + +
55G PRO* 3.7 1.7 - - - +
64G ARG* 3.2 26.3 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il