Contacts of the helix formed by residues 25 - 36 (chain I) in PDB entry 2WWB
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 25 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24I VAL* 1.4 71.7 - - - +
26I PHE* 1.4 59.9 + - - +
27I LYS* 3.4 9.7 + - - +
28I ASN* 3.0 39.8 + - - -
29I THR* 2.7 32.7 + - - -
86I LYS* 5.5 3.9 - - - +
87I SER* 4.2 4.5 - - - -
142I SER* 3.1 32.1 + - - -
144I SER* 4.5 0.2 - - - -
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Residues in contact with PHE 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I SER* 1.4 71.2 + - - +
27I LYS* 1.4 69.9 + - + +
29I THR* 4.5 0.2 - - - -
30I ARG* 3.2 61.0 + - - +
119I VAL* 4.0 17.2 - - + +
121I GLN* 3.5 53.2 - - + -
123I PRO 5.3 1.6 - - - +
124I LYS* 4.5 13.2 - - + -
142I SER* 4.2 3.2 - - - -
143I PRO* 3.5 16.4 + - + +
144I SER* 3.2 24.2 - - - +
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Residues in contact with LYS 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I SER* 3.4 7.6 + - - +
26I PHE* 1.4 87.0 - - + +
28I ASN* 1.4 61.5 + - - +
30I ARG* 3.2 25.7 - - - +
31I GLU* 3.8 10.7 - - - +
63I PHE* 4.2 39.6 - - + +
124I LYS* 6.1 2.2 - - - +
140I GLU* 3.3 24.0 + - - +
142I SER* 3.2 28.3 + - - -
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Residues in contact with ASN 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I SER* 3.0 22.9 + - - +
27I LYS* 1.4 79.7 - - - +
29I THR* 1.4 63.7 + - - +
30I ARG 3.3 0.7 - - - -
31I GLU* 3.4 6.2 + - - +
32I THR* 3.2 22.9 + - - -
60I PHE* 3.9 21.5 - - + -
63I PHE* 3.9 20.9 - - - -
82I ARG* 5.2 5.1 - - - +
84I PRO* 4.0 26.0 - - + +
87I SER* 3.4 18.2 - - - +
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Residues in contact with THR 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I VAL 3.9 0.5 + - - -
25I SER 2.7 24.5 + - - -
26I PHE 4.5 0.7 - - - -
28I ASN* 1.4 75.9 - - - +
30I ARG* 1.4 58.1 + - - +
32I THR* 3.7 5.3 - - - -
33I ALA* 2.9 27.5 + - + +
87I SER* 3.1 15.7 + - - -
90I PHE* 3.5 31.0 - - + -
91I VAL* 4.2 13.7 - - + -
119I VAL* 4.5 7.2 - - + -
146I ILE* 3.6 28.5 - - + -
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Residues in contact with ARG 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I PHE* 3.2 59.9 + - - +
27I LYS* 3.2 24.2 - - - +
29I THR* 1.4 76.1 - - - +
31I GLU* 1.4 64.4 + - + +
33I ALA* 3.5 4.8 + - - +
34I GLN* 3.0 29.6 + - - +
63I PHE* 6.4 0.9 - - - -
119I VAL* 3.7 28.1 + - + +
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Residues in contact with GLU 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I LYS 3.8 13.2 - - - +
28I ASN 3.4 9.1 + - - +
29I THR 3.3 0.2 - - - -
30I ARG* 1.4 82.7 - - + +
32I THR* 1.4 58.0 + - - +
34I GLN* 3.6 6.9 + - - +
35I ALA* 3.0 28.2 + - - +
58I ILE* 4.8 2.0 - - - -
59I PRO 4.3 3.1 - - - +
60I PHE* 3.6 29.0 - - + -
61I ARG* 3.1 40.2 + - - +
62I ARG* 3.2 14.0 + - - +
63I PHE* 3.1 30.9 + - + +
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Residues in contact with THR 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I ASN 3.2 15.7 + - - -
29I THR* 3.3 10.5 + - - -
31I GLU* 1.4 74.1 - - - +
33I ALA* 1.4 57.2 + - - +
35I ALA* 3.1 14.4 + - - +
36I ILE* 3.1 27.8 + - + +
48I LEU* 4.4 11.4 - - + -
58I ILE* 3.9 25.3 - - + +
60I PHE* 5.3 2.6 - - - -
84I PRO* 5.8 1.4 - - - +
87I SER* 4.2 14.5 - - - +
88I VAL* 5.7 3.9 - - + +
91I VAL* 3.8 28.0 - - + -
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Residues in contact with ALA 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I THR* 2.9 19.1 + - + +
30I ARG* 3.6 8.3 - - - +
31I GLU 3.4 0.2 - - - -
32I THR* 1.4 75.5 - - - +
34I GLN* 1.3 57.0 + - - +
36I ILE* 3.2 5.7 - - - +
37I ASN* 3.0 18.9 + - - -
91I VAL* 5.5 2.0 - - - +
117I ILE* 3.1 53.5 - - + +
118I GLN* 5.2 1.1 - - - +
119I VAL* 5.5 3.6 - - + -
146I ILE* 4.5 7.9 - - + -
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Residues in contact with GLN 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I ARG 3.0 18.2 + - - +
31I GLU* 3.9 6.7 - - - +
33I ALA* 1.3 74.7 - - - +
35I ALA* 1.4 57.5 + - - +
37I ASN* 3.0 18.2 + - - +
61I ARG* 3.2 42.3 + - + +
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Residues in contact with ALA 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I GLU 3.0 18.6 + - - +
32I THR 3.1 6.6 + - - +
34I GLN* 1.4 78.1 - - - +
36I ILE* 1.4 61.4 + - - +
37I ASN* 3.3 11.1 + - - +
39I TRP* 5.0 3.6 - - - -
58I ILE* 3.6 32.9 - - + +
59I PRO* 4.1 2.0 - - + +
61I ARG* 3.5 28.4 + - - +
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Residues in contact with ILE 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I THR* 3.1 20.5 + - + +
33I ALA 3.2 17.3 - - - +
35I ALA* 1.4 74.5 - - - +
37I ASN* 1.4 57.8 + - - +
39I TRP* 2.9 28.3 - - - -
44I ALA* 4.2 17.5 - - + +
48I LEU* 4.7 8.7 - - + -
58I ILE* 4.2 10.6 - - + +
91I VAL* 4.2 24.9 - - + -
95I LEU* 5.1 8.1 - - + -
114I VAL* 3.9 26.7 - - + -
117I ILE* 3.5 28.3 - - + -
148I LEU* 4.5 3.6 - - + -
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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