Contacts of the strand formed by residues 92 - 107 (chain A) in PDB entry 5OAB
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 ARG 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ASN* 3.5 16.7 - - - +
83A LEU* 3.4 6.1 - - - +
84A THR* 2.8 31.0 + - - +
85A SER* 3.0 30.9 + - - +
90A GLN* 4.0 10.5 - - + +
91A CYS* 1.3 78.1 - - - +
93A TYR* 1.3 57.6 + - - +
204A PO4 2.8 47.2 + - - +
206A PO4 3.0 44.8 + - - -
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Residues in contact with TYR 93 (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 CYS* 3.7 19.7 - - + +
24A ASN* 2.8 26.8 + - - +
27A MET* 3.6 41.1 - - + +
31A ASN* 3.0 20.3 + - - -
37A CYS* 3.8 3.6 - - - -
38A LYS 2.7 34.1 + - - -
39A HIS 4.5 1.3 - - - -
81A CYS* 3.9 9.0 - - + -
82A ARG 3.2 29.2 - - - +
83A LEU* 3.4 15.6 - - + +
84A THR* 3.8 6.6 + - - -
91A CYS* 3.6 24.7 - - + -
92A ARG* 1.3 77.7 - - - +
94A SER* 1.3 62.9 + - - +
204A PO4 5.0 5.2 + - - -
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Residues in contact with SER 94 (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 CYS* 3.8 2.1 - - - -
80A ASP 3.5 0.9 + - - +
81A CYS* 3.3 5.7 - - - -
82A ARG* 2.8 50.9 + - - +
84A THR* 3.8 17.6 - - - +
93A TYR* 1.3 75.0 - - - +
95A ALA* 1.3 63.2 + - - +
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Residues in contact with ALA 95 (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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22A GLN* 5.8 2.9 - - - +
23A CYS* 3.6 21.5 - - + +
79A THR* 4.0 9.4 - - + -
80A ASP 3.3 4.7 - - - -
93A TYR 4.4 0.2 + - - -
94A SER* 1.3 79.5 - - - +
96A ALA* 1.3 62.7 + - - +
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Residues in contact with ALA 96 (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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79A THR* 3.6 4.1 - - - -
80A ASP* 2.9 49.2 + - + +
82A ARG* 6.5 0.7 - - - -
95A ALA* 1.3 76.6 - - - +
97A ALA* 1.3 65.8 + - - +
98A GLN* 3.7 5.1 + - + +
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Residues in contact with ALA 97 (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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78A MET 3.8 4.9 - - - +
79A THR* 4.8 4.7 - - - +
95A ALA 4.3 0.2 - - - -
96A ALA* 1.3 74.7 - - - +
98A GLN* 1.3 64.0 + - - +
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Residues in contact with GLN 98 (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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42A THR* 4.6 3.3 + - - +
77A ASN* 3.4 8.0 + - - +
78A MET* 2.8 56.9 + - + +
79A THR 4.6 0.2 - - - -
80A ASP* 3.6 34.2 + - - +
96A ALA* 4.0 8.2 - - + +
97A ALA* 1.3 82.4 - - - +
99A TYR* 1.3 62.5 + - - +
100A LYS* 4.1 21.7 - - + +
126A ILE* 3.9 23.0 - - - +
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Residues in contact with TYR 99 (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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75A PRO* 3.3 48.5 + - + +
76A VAL* 3.3 19.3 - - - -
77A ASN* 3.6 22.0 - - - +
98A GLN* 1.3 75.6 - - - +
100A LYS* 1.3 64.8 + - - +
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Residues in contact with LYS 100 (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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75A PRO* 3.6 9.5 - - - +
76A VAL* 2.9 26.1 + - - +
78A MET* 3.3 19.6 - - + +
98A GLN* 4.1 24.2 - - + +
99A TYR* 1.3 84.2 - - - +
101A PHE* 1.3 71.5 + - - +
126A ILE* 3.7 26.7 - - + -
127A LEU* 3.1 30.3 + - - +
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Residues in contact with PHE 101 (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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71A GLN* 3.7 19.5 - - + +
72A SER* 3.3 24.5 - - - +
73A SER 3.7 14.8 - - - -
74A LYS 3.6 20.6 - - - -
75A PRO* 3.9 21.3 - - + -
100A LYS* 1.3 76.9 - - - +
102A PHE* 1.3 61.4 + - - +
126A ILE* 3.4 7.3 - - - +
127A LEU* 2.9 58.1 + - + +
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Residues in contact with PHE 102 (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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44A LEU* 4.2 15.9 - - + -
46A ASP* 5.6 1.1 - - + -
50A ASN 5.2 0.9 - - - -
51A VAL* 4.0 26.0 - - + -
54A VAL* 4.0 15.0 - - + -
71A GLN* 4.0 0.3 - - - +
72A SER* 2.8 52.8 + - - -
76A VAL* 3.8 39.9 - - + -
78A MET* 4.5 0.9 - - + -
100A LYS 4.6 0.2 - - - -
101A PHE* 1.3 74.7 - - - +
103A ILE* 1.3 67.8 + - - +
104A VAL* 3.7 41.1 - - + -
123A LEU* 3.8 17.5 - - + -
125A SER 3.6 6.1 - - - +
126A ILE* 4.3 6.1 - - + -
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Residues in contact with ILE 103 (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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60A ILE* 4.4 13.2 - - + -
61A VAL 5.8 0.7 - - - +
69A CYS* 3.6 28.9 - - + -
70A HIS 3.3 8.5 - - - +
71A GLN* 4.1 25.6 - - + +
102A PHE* 1.3 85.5 - - - +
104A VAL* 1.3 61.1 - - - +
123A LEU* 3.8 3.3 - - - +
124A ASP* 2.8 36.6 + - + +
125A SER* 2.9 35.2 + - - +
126A ILE 4.7 0.2 - - - -
127A LEU* 4.3 21.1 - - + -
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Residues in contact with VAL 104 (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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11A PHE* 3.8 26.7 - - + -
44A LEU* 5.0 0.2 - - + -
51A VAL* 4.3 8.7 - - + +
54A VAL* 3.9 28.9 - - + -
55A CYS* 4.9 0.2 - - - -
69A CYS* 3.2 5.3 - - - -
70A HIS* 2.9 32.0 + - + -
102A PHE* 3.7 25.5 - - + -
103A ILE* 1.3 74.6 - - - +
105A ALA* 1.3 62.8 + - - +
106A CYS* 4.1 16.8 - - - -
120A PRO* 4.6 1.8 - - + -
122A HIS 3.3 12.8 - - - +
123A LEU* 4.4 5.4 - - + -
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Residues in contact with ALA 105 (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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62A CYS* 4.2 1.8 - - - -
64A ASN* 6.3 0.4 - - - +
68A ASN* 3.2 24.0 - - - +
69A CYS* 3.8 18.3 - - - -
104A VAL* 1.3 73.2 - - - +
106A CYS* 1.3 55.5 + - - +
120A PRO* 3.4 4.2 - - - +
121A VAL* 2.8 34.6 + - + -
122A HIS* 2.9 32.6 + - + +
124A ASP* 4.8 2.6 - - - +
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Residues in contact with CYS 106 (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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55A CYS* 2.1 59.0 - - + -
68A ASN* 3.0 31.2 + - - +
70A HIS* 3.8 14.5 + - - +
104A VAL* 4.1 10.1 - - - -
105A ALA* 1.3 81.0 - - - +
107A ASP* 1.3 65.9 + - - +
118A LEU* 4.1 11.4 - - + +
119A VAL 3.1 8.1 - - - +
120A PRO* 3.9 4.7 - - - -
121A VAL* 4.2 1.6 - - - -
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Residues in contact with ASP 107 (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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7A LYS* 4.9 2.9 + - - -
66A ARG* 2.8 43.2 + - - -
68A ASN* 3.1 7.7 + - - +
106A CYS* 1.3 80.6 - - - +
108A PRO* 1.3 81.9 - - + +
118A LEU* 3.7 7.6 - - - -
119A VAL* 2.8 31.0 + - - +
121A VAL* 3.8 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