Contacts of the helix formed by residues 39 - 50 (chain G) in PDB entry 3PHW
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 ASN 39 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G ASP* 2.8 20.4 + - - +
38G GLY* 1.3 77.9 + - - +
40G CYS* 1.3 64.8 + - - +
41G PHE 3.2 2.9 - - - -
42G TYR* 3.0 13.9 + - + +
43G HIS* 3.0 30.8 + - - +
58G TYR* 3.2 46.3 + - + -
62G LYS* 4.7 8.1 - - - +
96G ASP* 3.6 8.7 + - - +
97G ASN* 3.0 36.4 - - - +
98G GLU 4.2 2.6 + - - +
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Residues in contact with CYS 40 (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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34G GLN* 4.5 2.6 - - + +
35G PRO 4.4 4.7 - - - +
37G ASP* 3.7 6.0 + - - +
39G ASN* 1.3 78.2 - - - +
41G PHE* 1.3 63.6 + - - +
43G HIS* 3.5 12.7 - - - +
44G SER* 2.9 29.2 + - - -
151G HIS* 3.9 14.8 - - + -
152G PHE* 3.3 35.4 - - - +
75H GLY 3.4 4.0 - - - -
76H NEH 1.8 59.6 - - + +
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Residues in contact with PHE 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G ASN 3.0 1.0 + - - -
40G CYS* 1.3 81.5 - - - +
42G TYR* 1.3 88.7 + + + +
44G SER* 3.3 4.7 + - - -
45G ILE* 3.2 36.6 + - + +
100G GLY* 3.8 23.8 - - - +
101G SER 3.7 12.3 - - - -
104G GLU* 3.7 18.4 - - + -
105G ALA* 3.6 33.9 - - + -
108G LEU* 4.0 11.2 - - + -
118G ILE* 5.0 0.7 - - + -
144G LEU* 3.6 26.2 - - + -
152G PHE* 3.7 38.4 - + + -
76H NEH 4.1 0.6 - - - +
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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
----------------------------------------------------------
39G ASN* 3.0 17.4 + - + +
41G PHE* 1.3 94.3 - + + +
43G HIS* 1.3 66.8 + - - +
45G ILE* 3.4 1.6 + - - +
46G ALA* 3.0 26.2 + - - +
58G TYR* 3.7 26.7 - - + +
61G ILE* 3.9 24.2 - - + +
62G LYS* 3.5 39.0 - - + -
65G THR* 3.7 21.3 - - + -
93G MET* 3.6 15.7 + - - +
98G GLU* 3.9 20.0 + - - +
99G TRP 4.7 1.4 + - - -
100G GLY* 3.7 15.2 - - - -
104G GLU* 3.4 21.3 - - - +
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Residues in contact with HIS 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G GLN* 3.4 23.6 + - + +
35G PRO* 4.0 26.8 - - + +
37G ASP* 3.3 34.9 + - - -
39G ASN* 3.0 26.3 + - - +
40G CYS* 3.5 11.9 - - - +
42G TYR* 1.3 76.5 - - - +
44G SER* 1.3 56.8 + - - +
46G ALA* 3.3 4.2 + - - +
47G GLU* 3.0 24.6 + - - +
53G LYS* 3.7 8.7 - - - +
54G THR 4.9 0.6 + - - -
55G ASP* 3.4 33.8 + - + -
58G TYR* 3.4 24.3 - + - +
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Residues in contact with SER 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G GLN* 3.3 7.0 - - - +
40G CYS 2.9 18.7 + - - -
41G PHE* 3.5 6.5 - - - -
42G TYR 3.2 0.2 - - - -
43G HIS* 1.3 73.3 - - - +
45G ILE* 1.3 66.3 + - - +
47G GLU* 3.3 15.6 + - - +
48G LEU* 3.4 8.1 + - - +
144G LEU* 4.0 17.0 - - - -
152G PHE* 3.5 3.1 + - - -
153G ASP* 3.1 39.9 + - - -
154G ALA* 3.8 12.4 - - - +
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Residues in contact with ILE 45 (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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41G PHE* 3.2 35.8 + - + +
42G TYR 3.4 4.7 + - - +
44G SER* 1.3 76.0 - - - +
46G ALA* 1.3 62.2 + - - +
48G LEU* 3.1 4.9 + - - +
49G THR* 2.8 40.0 + - + +
61G ILE* 3.9 31.2 - - + -
108G LEU* 4.6 3.6 - - + -
112G MET* 4.3 11.7 - - - -
114G ILE* 5.2 1.6 - - + -
116G ILE* 4.2 12.6 - - + -
142G VAL* 4.1 13.9 - - + -
144G LEU* 3.6 31.6 - - + -
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Residues in contact with ALA 46 (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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42G TYR 3.0 18.6 + - - +
43G HIS* 3.7 4.7 - - - +
45G ILE* 1.3 76.4 - - - +
47G GLU* 1.3 65.9 + - - +
49G THR* 3.8 6.5 - - - -
50G MET* 2.9 50.7 + - - +
53G LYS* 3.9 5.4 - - + +
57G SER* 3.8 22.4 - - - +
58G TYR 4.4 0.7 - - - +
61G ILE* 3.9 8.9 - - + +
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Residues in contact with GLU 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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32G VAL* 3.5 29.2 - - + +
34G GLN* 3.4 13.9 + - - +
43G HIS 3.0 13.8 + - - +
44G SER 3.4 11.2 - - - +
46G ALA* 1.3 78.3 - - - +
48G LEU* 1.3 59.1 + - + +
50G MET 4.4 6.4 - - - +
53G LYS* 3.1 40.4 + - - +
154G ALA* 3.9 9.4 - - + -
156G ARG* 3.1 44.3 + - - +
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Residues in contact with LEU 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 SER 3.4 5.1 + - - +
45G ILE 3.1 6.9 + - - +
46G ALA 3.1 0.4 - - - -
47G GLU* 1.3 78.4 - - + +
49G THR* 1.3 61.1 + - - +
50G MET 3.8 0.2 - - - -
142G VAL* 3.9 23.6 - - + +
143G ASN 3.2 39.9 - - - +
144G LEU* 4.2 7.0 - - + -
154G ALA* 4.0 15.7 - - + -
155G LEU 3.4 20.6 - - - +
156G ARG* 3.7 35.6 + - + +
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Residues in contact with THR 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G ILE* 2.8 31.0 + - + +
46G ALA* 3.8 0.3 - - - -
48G LEU* 1.3 81.5 - - + +
50G MET* 1.3 71.7 + - - +
51G PRO* 4.1 4.9 - - - +
61G ILE* 3.9 10.2 - - - +
112G MET* 4.0 22.9 - - + +
114G ILE* 4.3 7.4 - - + -
142G VAL* 3.8 23.8 - - + -
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Residues in contact with MET 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ALA* 2.9 31.5 + - + +
47G GLU 4.4 4.2 - - - +
48G LEU 3.8 0.2 - - - -
49G THR* 1.3 91.8 - - - +
51G PRO* 1.3 74.2 - - + +
52G ASN 3.7 0.5 + - - -
53G LYS* 3.7 13.8 + - + +
57G SER* 3.4 33.7 - - - +
60G TYR* 3.5 41.3 - - + -
61G ILE* 3.9 9.6 - - + -
112G MET* 6.3 0.2 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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