Contacts of the helix formed by residues 38 - 54 (chain G) in PDB entry 4GEK
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 GLY 38 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASN* 5.8 1.1 - - - -
36G VAL 3.3 0.6 + - - -
37G PRO* 1.3 73.1 - - - +
39G TYR* 1.3 65.2 + - - +
40G SER* 3.3 3.4 - - - -
41G ASN* 3.0 14.5 + - - +
42G ILE* 3.0 25.0 + - - +
184G PHE* 4.9 3.2 - - - -
230G PHE* 3.7 22.9 - - - -
232G CYS* 4.4 4.8 - - - +
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Residues in contact with TYR 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G PHE* 4.9 2.4 - - - -
29G PRO* 5.9 2.2 - - + -
32G ILE* 3.3 36.8 - - + +
33G GLN* 5.3 9.4 - - + -
36G VAL* 3.1 27.3 + - + +
37G PRO 3.3 1.2 + - - -
38G GLY* 1.3 75.3 - - - +
40G SER* 1.4 64.0 + - - +
42G ILE* 3.1 10.1 + - - +
43G ILE* 2.9 40.4 + - + +
69G ALA* 3.1 20.1 - - + +
132G ASN* 3.7 18.8 - - - -
133G PHE* 4.1 20.9 - + - -
303G GEK 2.7 30.5 + - + -
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Residues in contact with SER 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G GLN* 4.5 16.3 + - - -
38G GLY 3.3 1.1 - - - -
39G TYR* 1.4 86.4 - - - +
41G ASN* 1.3 71.6 + - - +
43G ILE* 3.3 7.6 + - - +
44G SER* 3.0 26.0 + - - -
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Residues in contact with ASN 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASN* 2.8 31.3 + - - +
232A CYS* 5.7 3.8 - - - -
38G GLY* 3.0 14.0 + - - +
40G SER* 1.3 85.0 + - - +
42G ILE* 1.3 59.2 + - - +
44G SER* 3.1 8.7 + - - -
45G MET* 2.9 36.3 + - - +
230G PHE* 3.7 24.0 - - + -
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Residues in contact with ILE 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G PRO 5.1 2.5 - - - +
38G GLY 3.0 17.7 + - - +
39G TYR* 3.5 5.8 - - - +
41G ASN* 1.3 76.6 - - - +
43G ILE* 1.3 63.7 + - - +
45G MET* 3.1 9.3 + - + +
46G ILE* 2.9 30.3 + - + +
132G ASN* 3.3 25.8 - - - +
133G PHE* 3.7 30.3 - - + -
161G VAL* 5.1 0.2 - - + -
163G SER* 3.6 8.5 - - - +
229G TRP* 5.5 1.6 - - + +
230G PHE* 3.5 37.5 - - + -
235G PHE 5.7 0.4 - - - -
236G GLY* 4.5 4.3 - - - +
237G SER* 4.3 15.9 - - - +
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Residues in contact with ILE 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G TYR* 2.9 48.2 + - + +
40G SER* 3.7 9.9 - - - +
41G ASN 3.3 0.2 - - - -
42G ILE* 1.3 75.1 - - - +
44G SER* 1.3 58.9 + - - +
46G ILE* 3.4 7.0 + - + +
47G GLY 3.2 7.1 + - - -
69G ALA* 4.0 9.0 - - + +
70G ALA* 3.9 27.6 - - + +
73G SER* 2.7 42.4 + - - +
76G ARG* 4.7 7.4 - - - +
132G ASN* 3.7 23.3 - - - +
303G GEK 4.0 0.2 - - - +
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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
----------------------------------------------------------
40G SER 3.0 14.5 + - - -
41G ASN* 3.1 11.5 + - - -
43G ILE* 1.3 74.0 - - - +
45G MET* 1.3 68.9 + - - +
47G GLY* 3.3 2.4 + - - +
48G MET* 3.0 31.1 + - - +
73G SER* 4.5 2.2 - - - -
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Residues in contact with MET 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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232A CYS* 4.1 9.4 - - - -
233A PHE* 3.6 40.8 - - + +
41G ASN* 2.9 23.5 + - + +
42G ILE* 3.6 7.0 - - - +
44G SER* 1.3 79.6 - - - +
46G ILE* 1.3 56.8 + - - +
48G MET* 3.1 10.2 + - - +
49G LEU 2.9 25.1 + - - -
229G TRP* 3.2 62.3 - - + +
230G PHE* 3.5 32.3 - - + -
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Residues in contact with ILE 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G ILE* 2.9 23.7 + - + +
43G ILE* 3.5 11.9 - - - +
45G MET* 1.3 77.4 - - - +
47G GLY* 1.3 56.2 + - - +
49G LEU* 3.3 2.2 + - - -
50G ALA* 2.9 27.7 + - - +
70G ALA* 4.3 14.4 - - + +
73G SER* 4.6 2.2 - - - +
74G VAL* 3.6 25.8 - - + -
128G MET* 3.6 12.5 - - + +
130G VAL* 4.0 19.5 - - + -
132G ASN* 3.7 34.1 - - + +
161G VAL* 4.0 23.1 - - + -
229G TRP* 4.5 5.6 - - + -
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Residues in contact with GLY 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G ILE 3.2 7.9 + - - -
44G SER 3.3 2.9 + - - -
45G MET 3.2 0.8 - - - -
46G ILE* 1.3 80.1 - - - +
48G MET* 1.3 61.3 + - - +
50G ALA* 3.2 2.5 + - - -
51G GLU* 3.2 8.7 + - - +
73G SER* 3.3 22.1 + - - -
77G ASN* 3.1 41.8 - - - +
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Residues in contact with MET 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A MET* 3.5 44.1 - - + +
183A ASP* 3.8 16.2 - - + +
184A PHE* 3.7 23.3 - - - +
187A ALA* 6.0 0.7 - - + -
233A PHE* 3.7 26.9 - - + -
44G SER* 3.0 23.8 + - - +
45G MET* 3.4 9.4 - - - +
47G GLY* 1.3 77.5 - - - +
49G LEU* 1.3 61.9 + - - +
51G GLU* 3.3 18.6 + - - +
52G ARG* 3.6 4.3 + - - +
77G ASN* 5.0 1.8 - - - +
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Residues in contact with LEU 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 3.8 22.0 - - + -
180A MET* 4.2 7.1 - - + -
45G MET 2.9 16.0 + - - +
46G ILE 3.7 4.5 - - - +
48G MET* 1.3 76.5 - - - +
50G ALA* 1.3 63.3 + - - +
52G ARG 3.0 3.3 + - - -
53G PHE* 2.9 55.4 + - + +
128G MET* 4.0 8.1 - - + -
159G ALA* 4.0 20.0 - - + -
161G VAL* 3.6 31.2 - - + -
229G TRP* 3.7 20.0 - - + -
239G VAL* 4.1 6.5 - - + -
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Residues in contact with ALA 50 (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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46G ILE 2.9 14.4 + - - +
47G GLY 3.2 9.2 + - - +
49G LEU* 1.3 77.2 - - - +
51G GLU* 1.3 62.8 + - - +
53G PHE 4.4 0.2 - - - +
54G VAL* 3.0 40.1 + - + +
74G VAL* 4.0 32.3 - - + +
77G ASN* 4.1 5.3 - - + +
128G MET* 3.8 14.8 - - - -
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Residues in contact with GLU 51 (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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183A ASP* 6.0 0.9 - - - +
186A ARG* 4.1 18.4 + - - -
47G GLY 3.2 10.3 + - - +
48G MET* 3.6 11.4 - - - +
49G LEU 3.1 0.8 - - - -
50G ALA* 1.3 77.8 - - - +
52G ARG* 1.3 62.5 + - + +
54G VAL 4.9 3.6 + - - +
77G ASN* 3.0 34.6 + - - +
79G HIS* 2.7 35.6 + - + -
80G HIS* 5.3 4.7 + - - -
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Residues in contact with ARG 52 (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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176A LEU* 5.5 0.7 - - - -
179A ASN* 3.7 41.2 + - - +
180A MET* 3.7 16.8 - - + -
182A HIS* 3.9 13.7 + - - -
183A ASP* 2.7 41.8 + - - +
186A ARG* 4.9 1.2 - - - +
48G MET 3.6 2.9 + - - +
49G LEU 3.0 4.0 + - - +
51G GLU* 1.3 83.8 - - + +
53G PHE* 1.3 80.8 + - + +
54G VAL 3.7 1.1 - - - -
55G GLN* 3.9 11.3 + - - -
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Residues in contact with PHE 53 (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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172A LYS* 6.4 1.8 - - - -
176A LEU* 3.6 29.2 - - + -
49G LEU* 2.9 31.9 + - + +
52G ARG* 1.3 93.9 - - + +
54G VAL* 1.3 65.3 + - - +
55G GLN* 3.2 15.6 + - - +
127G SER* 3.4 22.3 - - - +
128G MET* 4.8 5.8 - - - -
157G GLY 3.4 26.5 - - - +
158G GLY* 5.7 0.2 - - - -
159G ALA* 3.7 18.8 - - + -
241G LEU* 3.7 31.2 - - + -
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Residues in contact with VAL 54 (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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50G ALA* 3.0 37.3 + - + +
51G GLU 4.9 2.3 - - - +
52G ARG 5.1 1.0 - - - -
53G PHE* 1.3 76.1 - - - +
55G GLN* 1.3 62.7 + - - +
58G THR* 4.3 0.9 - - - +
60G VAL* 3.5 31.4 - - + -
74G VAL* 4.3 3.4 - - + -
78G ILE* 3.8 24.9 - - + -
80G HIS* 3.2 22.7 + - + -
83G CYS* 3.9 19.1 - - + -
127G SER* 3.4 9.6 - - - +
128G MET* 4.0 11.7 - - + -
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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
------------------------------------------------------------
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