Contacts of the strand formed by residues 32 - 41 (chain A) in PDB entry 2YB6
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 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ARG* 5.2 4.0 + - - -
29A SER* 2.7 33.0 + - - +
30A GLU 3.6 0.2 - - - -
31A ASN* 1.3 87.3 - - - +
33A ILE* 1.3 64.8 + - - +
34A MET* 2.9 31.5 + - - +
35A GLN* 3.0 28.0 + - + +
58A GLU* 5.5 0.8 + - - -
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Residues in contact with ILE 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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6A ARG* 3.4 55.7 - - + +
9A LEU* 3.7 23.3 - - + +
10A MET* 3.7 39.7 - - + +
28A PRO* 3.9 27.6 - - + -
29A SER 4.5 0.4 + - - -
32A ASN* 1.3 73.3 + - - +
34A MET* 1.3 62.9 + - + +
35A GLN 3.3 0.2 - - - -
36A TRP* 2.9 28.9 + - - +
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Residues in contact with MET 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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5A ALA* 4.1 6.1 - - + -
6A ARG* 3.9 30.7 - - + +
9A LEU* 3.9 9.0 - - + -
32A ASN* 2.9 20.5 + - - +
33A ILE* 1.3 78.6 - - + +
35A GLN* 1.3 55.9 + - - +
57A ILE 3.7 0.2 - - - +
58A GLU* 3.6 5.8 - - - +
59A PHE* 2.8 48.2 + - - +
60A SER* 3.6 37.2 - - - +
61A GLU* 3.5 37.9 - - + +
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Residues in contact with GLN 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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29A SER* 2.8 35.0 + - - +
32A ASN* 3.0 23.1 + - + +
33A ILE 3.3 0.2 - - - -
34A MET* 1.3 78.1 - - - +
36A TRP* 1.3 65.2 + - - +
37A ASN* 5.2 5.6 - - - +
56A VAL* 3.7 21.7 - - + +
57A ILE 3.4 2.2 - - - -
58A GLU* 2.7 35.5 - - - +
71A ARG* 4.8 5.2 + - - +
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Residues in contact with TRP 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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9A LEU* 3.5 32.0 - - + +
12A ASP* 4.1 0.4 - - + -
13A PHE* 3.6 32.5 - + + -
16A LEU* 4.3 4.7 - - + -
26A GLY* 4.0 14.1 - - - -
27A ALA* 3.3 23.1 - - - +
28A PRO* 3.6 25.1 - - + +
33A ILE* 2.9 30.1 + - - +
35A GLN* 1.3 76.2 - - - +
37A ASN* 1.3 63.3 + - - +
56A VAL* 3.3 10.6 - - - +
57A ILE* 2.9 46.3 + - + -
59A PHE* 3.5 24.2 - + - -
102A VAL* 3.7 36.1 - - + -
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Residues in contact with ASN 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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26A GLY* 3.2 1.9 - - - -
27A ALA* 3.0 32.1 + - + +
28A PRO 5.1 0.2 - - - -
29A SER* 4.1 21.7 - - - -
35A GLN* 5.2 6.6 - - - +
36A TRP* 1.3 77.6 + - - +
38A ALA* 1.3 60.9 + - - +
39A VAL* 5.7 0.4 - - - -
55A LEU 3.6 4.4 + - - +
56A VAL* 4.1 16.4 - - - +
73A LEU* 5.7 4.0 - - - +
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Residues in contact with ALA 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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25A SER 3.3 13.9 - - - +
26A GLY* 3.8 3.1 - - - -
37A ASN* 1.3 75.5 - - - +
39A VAL* 1.3 69.1 + - - +
54A LYS* 3.4 3.5 - - - +
55A LEU* 2.9 41.3 + - + +
57A ILE* 4.2 12.6 - - + -
106A LEU* 3.8 30.7 - - + -
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Residues in contact with VAL 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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23A GLY 3.7 0.7 - - - +
24A VAL* 3.4 4.3 - - - -
25A SER* 2.9 45.0 + - - +
37A ASN 5.7 0.4 - - - -
38A ALA* 1.3 80.5 - - - +
40A ILE* 1.3 69.3 + - - +
41A PHE* 4.0 26.9 - - + -
52A THR* 4.7 6.3 - - - -
53A PHE 3.2 16.8 - - - +
54A LYS* 5.0 10.1 - - + -
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Residues in contact with ILE 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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23A GLY 3.3 4.0 - - - +
24A VAL* 4.2 8.1 - - + -
39A VAL* 1.3 79.6 - - - +
41A PHE* 1.3 77.7 - - - +
53A PHE* 2.9 39.7 + - + +
55A LEU* 3.7 22.4 - - + +
72A PHE* 5.0 1.8 - - + -
106A LEU* 3.5 36.3 - - + +
109A ILE* 3.6 27.4 - - + -
110A GLN* 3.7 24.2 - - + +
113A LEU* 4.5 11.0 - - + -
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Residues in contact with PHE 41 (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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23A GLY* 2.7 35.4 + - - +
25A SER* 5.7 2.9 - - - -
39A VAL* 4.0 20.4 - - + -
40A ILE* 1.3 79.1 - - - +
42A GLY* 1.3 70.7 + - - +
43A PRO 3.5 0.2 - - - -
50A ASP* 6.0 2.7 - - - -
51A GLY 3.3 7.0 - - - +
52A THR* 3.6 28.0 - - + +
110A GLN* 3.0 21.0 + - - -
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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