Contacts of the helix formed by residues 28 - 40 (chain A) in PDB entry 2I91
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 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLN 3.4 3.2 + - - -
27A VAL* 1.3 91.8 - - - +
29A ASP* 1.3 64.9 + - - +
30A MET* 3.5 6.4 + - - +
31A ASN* 2.9 33.9 + - - +
32A ARG* 2.9 5.0 + - - +
518A ASP* 5.2 0.8 + - - +
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Residues in contact with ASP 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLN* 5.1 2.1 - - - +
27A VAL 4.5 4.2 - - - +
28A SER* 1.3 71.9 - - - +
30A MET* 1.3 57.0 + - - +
32A ARG* 3.0 11.0 + - - +
33A LEU* 2.9 27.7 + - - +
60A ALA* 3.7 15.9 - - + +
63A ARG* 2.8 52.2 + - - +
64A LEU* 3.5 28.6 + - + +
67A ASP* 4.8 3.1 - - - +
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Residues in contact with MET 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A SER* 3.2 7.2 + - - +
29A ASP* 1.3 77.2 - - - +
31A ASN* 1.3 65.2 + - - +
33A LEU* 3.1 34.2 + - + +
34A ARG* 3.3 32.9 + - - +
64A LEU* 3.9 14.3 - - + +
69A LYS* 4.5 12.1 - - + -
72A GLU* 2.9 57.4 - - + +
73A VAL* 3.8 21.3 - - + +
76A GLU* 5.1 3.8 - - + +
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Residues in contact with ASN 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 3.6 13.0 - - + -
28A SER* 2.9 30.1 + - - +
30A MET* 1.3 77.8 - - - +
32A ARG* 1.3 60.8 + - - +
34A ARG* 3.2 30.8 + - - +
35A ARG* 3.0 29.6 + - - +
517A LEU* 5.6 1.4 - - - +
518A ASP* 2.6 41.1 - - + +
519A ILE 5.6 0.2 - - - -
520A CYS* 5.4 0.3 - - - +
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Residues in contact with ARG 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLN* 4.9 10.2 + - - -
27A VAL* 3.5 11.4 - - + +
28A SER 2.9 12.1 + - - +
29A ASP* 3.0 13.4 + - - +
31A ASN* 1.3 73.6 - - - +
33A LEU* 1.3 66.5 + - - +
35A ARG* 4.2 6.1 - - - -
36A PHE* 2.9 23.7 + - - +
53A LEU* 3.9 1.4 - - - +
56A GLU* 2.7 60.6 + - - +
57A ASN* 3.5 17.7 + - - +
60A ALA* 4.3 18.1 - - + +
63A ARG* 5.6 3.0 - - - +
503A SER 2.9 26.8 + - - +
504A ASN* 3.5 9.5 - - - +
505A GLY* 3.3 27.7 - - - +
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASP 2.9 11.4 + - - +
30A MET* 3.1 31.4 - - - +
31A ASN 3.1 0.2 - - - -
32A ARG* 1.3 77.5 - - - +
34A ARG* 1.3 58.4 + - - +
36A PHE* 3.2 13.6 + - + +
37A LEU* 2.8 52.4 + - + +
61A LEU* 4.7 14.6 - - + -
64A LEU* 4.5 5.6 - - + -
73A VAL* 4.1 30.5 - - + +
76A GLU* 4.1 26.5 - - + -
77A ILE* 5.0 1.3 - - + -
95A ALA* 4.8 9.2 - - + -
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Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A MET* 3.3 43.6 + - - +
31A ASN* 3.2 29.8 + - - +
33A LEU* 1.3 75.3 - - + +
35A ARG* 1.3 66.0 + - - +
37A LEU* 3.1 8.8 + - + +
38A CYS* 3.1 27.0 + - - -
72A GLU* 5.0 3.4 + - - -
76A GLU* 3.4 33.8 + - + +
80A PHE* 3.8 26.7 - - + -
85A ARG* 5.5 1.3 - - - +
518A ASP 5.7 0.2 + - - -
520A CYS* 4.1 13.5 - - + +
523A ASP* 5.4 1.6 - - - -
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Residues in contact with ARG 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 2.8 28.5 - - - +
31A ASN* 3.0 19.9 + - + +
32A ARG* 3.7 13.7 - - - +
34A ARG* 1.3 75.5 - - - +
36A PHE* 1.3 58.7 + - - +
38A CYS* 3.1 0.3 + - - -
39A PHE* 2.8 33.6 + - - +
470A CYS* 4.3 6.8 - - - -
498A VAL* 5.5 2.0 + - - +
500A ALA* 3.1 32.1 - - + +
502A THR 3.4 22.7 - - - +
503A SER* 3.9 7.6 - - - -
504A ASN* 2.8 42.3 + - - -
506A PHE 2.8 32.1 + - - +
507A SER* 4.0 2.8 - - - +
518A ASP* 3.4 10.3 + - - -
519A ILE 5.0 2.9 + - - +
520A CYS* 3.5 17.2 - - + -
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Residues in contact with PHE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ARG 2.9 19.7 + - - +
33A LEU* 3.3 15.5 - - + +
35A ARG* 1.3 74.4 - - - +
37A LEU* 1.3 69.1 + - + +
40A GLY* 2.7 44.1 + - - -
41A SER* 3.5 22.7 - - - -
54A GLY* 5.5 1.6 - - - -
57A ASN* 3.5 36.1 - - + +
61A LEU* 5.8 4.7 - - + -
91A PRO* 3.3 40.1 - - + +
94A PHE* 4.1 24.5 - + + -
95A ALA* 4.8 5.4 - - + -
503A SER* 4.0 7.6 - - - -
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 2.8 38.4 + - + +
34A ARG* 3.1 8.5 + - - +
36A PHE* 1.3 78.2 - - + +
38A CYS* 1.3 60.0 + - - +
76A GLU* 4.6 1.8 - - + +
77A ILE* 4.5 15.0 - - + -
80A PHE* 3.9 44.0 - - + -
86A ALA* 3.4 18.0 - - + +
87A ALA 5.3 0.2 + - - -
88A LYS 4.2 5.0 + - - +
91A PRO* 3.9 20.0 - - - +
92A THR* 3.5 39.1 + - + +
95A ALA* 4.6 9.9 - - + -
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Residues in contact with CYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG 3.1 10.4 + - - -
37A LEU* 1.3 80.1 - - - +
39A PHE* 1.3 61.6 + - + +
80A PHE* 3.6 24.7 - - - -
85A ARG 4.1 5.2 - - - -
86A ALA* 4.4 6.3 - - - +
87A ALA* 4.8 5.4 + - - +
88A LYS 5.3 0.5 + - - -
91A PRO* 5.8 0.2 - - - -
386A LEU* 3.4 23.2 - - - +
520A CYS* 3.5 33.7 - - - -
521A GLY 3.9 8.3 - - - +
522A PHE* 3.8 21.4 - - + +
523A ASP* 3.9 9.0 - - - -
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Residues in contact with PHE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ARG 2.8 26.4 + - - +
38A CYS* 1.3 74.0 - - - +
40A GLY* 1.3 68.1 + - - +
41A SER* 3.6 0.9 + - - -
42A GLU* 4.8 4.5 + - - +
91A PRO* 5.0 0.7 - - - -
385A VAL* 3.6 28.9 - - + -
386A LEU* 3.2 28.6 + - + +
395A VAL* 4.9 1.3 - - + -
500A ALA 3.2 26.2 - - - -
501A MET* 3.5 29.8 - - + -
502A THR* 3.6 26.2 - - - -
503A SER 4.4 0.7 - - - +
520A CYS* 3.6 10.1 - - - -
521A GLY* 3.0 31.0 - - - -
522A PHE* 4.3 11.0 - + + -
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Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 2.7 33.4 + - - -
38A CYS 3.8 0.6 - - - -
39A PHE* 1.3 76.6 - - - +
41A SER* 1.3 61.4 + - - -
42A GLU* 6.0 1.3 - - - -
53A LEU* 4.3 0.9 - - - +
91A PRO* 3.5 21.2 - - - +
503A SER* 2.9 24.3 + - - -
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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
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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