Contacts of the helix formed by residues 38 - 50 (chain C) in PDB entry 1W1W
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C SER* 4.1 0.4 - - - -
15C TYR* 2.8 24.9 + - - -
36C GLY 3.3 0.4 - - - -
37C SER* 1.3 79.6 + - - +
39C LYS* 1.3 66.5 + - - +
41C ASN* 3.4 8.8 + - - -
42C MET 3.2 10.7 + - - -
1204C VAL* 3.9 2.0 - - - -
1213C SER* 3.8 6.1 - - - -
2224C AGS 3.1 26.2 + - - -
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Residues in contact with LYS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ILE* 3.8 15.9 - - + +
32C ILE* 3.4 12.8 - - - +
33C GLY* 3.0 33.6 + - - +
34C PRO 2.9 20.2 + - - -
37C SER* 3.6 9.2 - - - +
38C GLY* 1.3 73.7 - - - +
40C SER* 1.3 62.6 + - - +
42C MET* 2.9 25.9 + - - +
43C MET 3.3 4.2 + - - -
1158C GLU* 5.6 0.4 - - - -
1188C ILE* 3.6 33.4 - - + +
1189C SER 5.0 1.6 - - - -
1190C LEU* 4.2 7.9 - - - -
1204C VAL* 3.9 14.1 - - + -
2224C AGS 2.7 50.4 + - - +
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Residues in contact with SER 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LYS* 1.3 72.0 - - - +
41C ASN* 1.3 67.5 + - - +
43C MET* 2.9 5.2 + - - +
44C ASP* 2.8 29.2 + - - +
151C GLN* 2.8 9.6 + - - +
1157C ASP* 2.9 21.2 + - - -
1188C ILE* 4.2 4.2 - - - +
2001C MG 2.0 30.9 - - - -
2224C AGS 3.0 17.3 + - - -
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Residues in contact with ASN 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PHE* 3.6 7.8 - - - -
13C LYS* 3.1 43.8 + - + -
14C SER* 3.2 16.0 + - - +
15C TYR* 4.0 12.1 - - + -
38C GLY* 3.5 8.3 - - - +
39C LYS 3.2 0.2 - - - -
40C SER* 1.3 72.2 - - - +
42C MET* 1.3 62.9 + - - +
44C ASP* 3.1 11.4 + - - +
45C ALA* 3.0 18.0 + - - +
2224C AGS 2.6 64.7 + - - +
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Residues in contact with MET 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 3.9 23.1 - - + -
9C LEU* 4.7 10.1 - - - -
15C TYR* 3.1 31.8 - - + +
21C VAL* 4.0 34.5 - - + -
23C PHE* 4.3 5.8 - - + -
31C ILE* 3.7 31.2 - - + -
38C GLY 3.2 2.4 + - - +
39C LYS* 2.9 17.7 + - - +
41C ASN* 1.3 76.4 - - - +
43C MET* 1.3 62.5 + - - +
45C ALA* 3.2 14.1 + - - +
46C ILE* 3.3 15.6 + - + +
1202C VAL* 4.6 5.6 - - + -
1204C VAL* 4.9 3.1 - - + -
1215C ILE* 4.9 4.5 - - + -
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Residues in contact with MET 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ILE* 5.7 1.3 - - - +
39C LYS 3.3 2.2 + - - -
40C SER* 2.9 9.2 + - - +
42C MET* 1.3 74.2 - - - +
44C ASP* 1.3 69.4 + - - +
45C ALA 3.0 1.8 - - - -
46C ILE* 2.8 18.5 + - + +
47C SER* 2.9 13.7 + - - -
148C LEU* 3.8 20.0 - - + -
149C VAL 3.6 28.9 - - - +
150C PHE* 3.8 26.9 - - + +
1155C VAL* 3.2 49.4 - - + +
1157C ASP* 4.1 19.3 - - - +
1188C ILE* 4.1 13.6 - - + +
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Residues in contact with ASP 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PHE* 3.6 13.8 - - + -
13C LYS* 2.9 30.2 + - + -
40C SER* 2.8 19.4 + - - +
41C ASN* 3.1 17.9 - - - +
43C MET* 1.3 78.7 - - - +
45C ALA* 1.3 53.5 + - - +
47C SER* 3.5 7.4 + - - -
48C PHE* 3.0 28.4 + - - +
65C LEU* 5.7 2.0 - - + -
150C PHE* 3.9 20.3 - - - -
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Residues in contact with ALA 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C LEU* 5.1 1.8 - - + -
9C LEU* 3.6 34.5 - - + -
12C PHE* 3.3 25.1 - - + -
41C ASN 3.0 6.8 + - - +
42C MET* 3.3 12.3 - - - +
43C MET 3.0 0.6 - - - -
44C ASP* 1.3 75.4 - - - +
46C ILE* 1.3 65.8 + - - +
48C PHE* 3.1 3.0 + - - +
49C VAL* 3.0 25.1 + - - +
94C VAL* 3.7 8.2 - - + +
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Residues in contact with ILE 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 4.1 22.2 - - + -
7C LEU* 3.6 33.0 - - + -
23C PHE* 4.7 4.0 - - + -
31C ILE* 5.4 1.1 - - + -
42C MET* 3.7 12.6 - - + +
43C MET* 2.8 10.1 + - + +
45C ALA* 1.3 78.4 - - - +
47C SER* 1.3 64.0 + - - +
49C VAL* 3.0 24.6 - - + +
50C LEU* 3.3 26.9 - - + +
148C LEU* 4.8 3.6 - - + -
1153C PHE* 4.6 2.5 - - + -
1155C VAL* 4.1 35.7 - - + -
1186C ILE* 4.4 12.3 - - + -
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Residues in contact with SER 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C MET* 2.9 12.4 + - - +
44C ASP* 3.5 8.5 + - - -
46C ILE* 1.3 77.1 - - - +
48C PHE* 1.3 65.0 + - - +
50C LEU* 3.3 3.5 + - - -
51C GLY 3.2 5.4 + - - -
52C VAL* 3.2 36.1 + - - +
148C LEU* 3.8 22.4 - - - +
150C PHE* 3.7 32.0 - - - -
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Residues in contact with PHE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PHE* 3.9 8.7 - + + -
44C ASP 3.0 16.4 + - - +
45C ALA 3.3 4.7 - - - +
46C ILE 3.1 0.2 - - - -
47C SER* 1.3 80.1 + - - +
49C VAL* 1.3 62.9 + - - +
51C GLY 2.8 18.4 + - - -
52C VAL 4.8 2.0 - - - +
62C LEU* 5.0 2.9 - - + -
65C LEU* 3.8 18.4 - - + -
93C TYR* 4.9 1.6 - - - -
94C VAL* 3.7 24.5 - - + -
109C ARG* 2.9 87.5 + - + +
110C ILE 4.3 1.1 - - - -
111C ILE* 3.1 44.6 - - + -
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Residues in contact with VAL 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 4.9 2.7 - - + -
45C ALA 3.0 11.1 + - - +
46C ILE* 3.0 26.5 - - + +
48C PHE* 1.3 73.9 - - - +
50C LEU* 1.3 61.8 + - + +
51C GLY 3.3 0.2 + - - -
94C VAL* 3.1 53.2 - - + +
95C LYS* 3.9 9.0 - - - +
96C ALA* 4.1 19.7 - - + -
107C LEU* 4.2 4.7 - - + +
109C ARG* 4.2 12.4 - - - +
119C TYR* 4.6 0.2 - - - -
131C TYR* 2.4 38.2 + - - +
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ILE* 3.3 26.1 + - + +
47C SER* 3.8 6.1 - - - +
48C PHE 3.1 1.4 - - - -
49C VAL* 1.3 84.5 - - + +
51C GLY* 1.3 55.4 + - - +
52C VAL* 4.7 1.6 - - + -
96C ALA* 5.6 2.9 - - + -
98C TYR* 6.6 0.2 - - + -
107C LEU* 4.6 9.6 - - + -
131C TYR* 4.3 2.7 - - - -
135C LEU* 3.3 39.2 - - + +
140C ILE* 4.1 6.1 - - + -
142C ILE* 2.8 40.4 - - + +
147C PHE* 3.5 35.0 - - + -
1153C PHE* 4.0 20.9 - - + -
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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