Contacts of the strand formed by residues 79 - 91 (chain A) in PDB entry 3QS1
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 THR 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A GLU* 3.8 14.8 - - + +
73A MET 3.5 3.4 - - - -
74A ASN* 2.5 31.0 + - - +
78A GLY* 1.3 73.4 - - - -
80A VAL* 1.3 84.2 + - - +
81A SER* 5.2 2.2 - - - -
106A ASP* 4.6 2.5 - - - +
107A THR 4.4 0.3 - - - +
109A GLY* 2.9 39.8 + - - +
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TRP* 3.7 35.4 - - + +
71A VAL 4.3 0.2 - - - -
72A GLU* 3.3 3.8 - - - -
73A MET* 2.8 54.7 + - + +
75A TYR* 4.6 3.3 - - + -
79A THR* 1.3 83.4 - - - +
81A SER* 1.3 60.9 + - - +
102A ILE* 5.9 0.9 - - + -
104A VAL* 3.8 20.0 - - + -
106A ASP 3.9 2.2 - - - +
107A THR* 4.2 18.2 - - + -
109A PHE* 3.6 32.0 + - + +
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL 3.1 13.7 + - - -
72A GLU* 4.1 14.7 + - - -
79A THR* 5.2 3.1 - - - -
80A VAL* 1.3 77.8 + - - +
82A GLY* 1.3 52.6 + - - +
104A VAL* 3.4 7.0 - - - +
105A THR* 2.7 29.5 + - - -
106A ASP* 2.9 39.4 + - - +
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Residues in contact with GLY 82 (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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70A LYS* 3.3 7.6 - - - +
71A VAL* 2.6 37.1 + - - -
81A SER* 1.3 76.4 + - - +
83A PHE* 1.3 57.9 + - - -
102A ILE* 4.3 3.1 - - - +
103A GLU 3.1 14.6 - - - -
104A VAL* 4.1 0.2 - - - -
105A THR* 3.6 14.4 - - - -
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Residues in contact with PHE 83 (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 SER* 4.1 1.8 - - - -
44A GLN* 4.5 12.8 - - + -
64A TYR* 5.4 4.5 - - - -
68A GLY* 3.5 24.5 - - - +
69A THR 3.2 13.7 - - - +
70A LYS* 3.9 7.0 - - + +
71A VAL* 4.3 5.6 - - - -
82A GLY* 1.3 78.2 - - - +
84A PHE* 1.3 72.1 + - - +
85A SER* 3.6 4.7 - - - -
102A ILE* 3.6 1.2 - - - -
103A GLU* 2.9 71.1 + - + -
105A THR* 3.8 26.2 - - + -
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Residues in contact with PHE 84 (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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37A ASN* 4.3 9.0 - - - -
67A ASP* 2.9 26.1 - - - +
68A GLY* 2.7 29.5 + - - -
69A THR* 2.9 28.1 + - - +
71A VAL* 3.3 28.3 - - + -
83A PHE* 1.3 73.1 - - - +
85A SER* 1.3 62.0 + - - +
100A LYS* 3.9 31.6 - - + -
101A PHE* 3.3 21.1 - - - -
102A ILE* 4.1 11.4 - - + -
130A ILE* 3.2 35.2 - - + -
131A GLY* 4.5 6.5 - - - -
133A VAL* 4.7 3.8 - - + -
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 3.6 23.6 + - - -
65A GLU 4.2 2.2 - - - -
67A ASP* 4.3 4.1 + - - +
83A PHE* 3.6 9.4 + - - -
84A PHE* 1.3 77.6 + - - +
86A LYS* 1.3 61.2 + - - +
100A LYS* 3.5 3.9 - - - +
101A PHE* 2.8 51.1 + - - +
103A GLU* 2.5 31.8 + - - +
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Residues in contact with LYS 86 (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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63A THR 4.9 0.2 - - - -
64A TYR* 3.4 3.7 - - - -
65A GLU* 2.8 63.6 + - + +
66A LYS 4.9 4.0 - - - +
67A ASP* 4.9 13.4 - - + +
85A SER* 1.3 73.5 - - - +
87A ASP* 1.3 63.7 + - - +
99A TYR 3.1 14.3 - - - +
100A LYS* 4.3 29.1 - - + +
101A PHE* 4.0 0.2 - - - -
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Residues in contact with ASP 87 (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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20A ILE* 5.0 0.2 - - + -
21A GLY* 3.2 21.0 + - - +
56A TYR* 2.8 21.7 + - + +
61A SER* 2.7 23.4 + - - -
63A THR* 3.3 23.4 + - - +
64A TYR* 3.5 7.0 - - - +
86A LYS* 1.3 74.6 - - - +
88A ILE* 1.3 85.1 + - - +
89A VAL* 3.7 1.3 + - - +
98A PRO* 3.6 2.4 - - - +
99A TYR* 2.7 31.5 + - - +
101A PHE* 3.4 22.8 - - + -
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Residues in contact with ILE 88 (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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20A ILE 3.9 0.3 - - - -
21A GLY 3.1 26.9 + - - +
22A ASP* 4.6 7.2 - - + +
63A THR* 3.5 27.4 - - + +
87A ASP* 1.3 95.9 + - - +
89A VAL* 1.3 61.2 + - - +
90A THR* 3.9 2.7 + - - +
95A SER* 3.6 21.8 - - - +
96A PHE* 3.4 33.9 - - - +
98A PRO* 4.0 9.9 - - + -
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Residues in contact with VAL 89 (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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18A ALA* 5.5 1.8 - - + -
19A GLN 3.4 11.9 - - - +
20A ILE* 3.9 27.1 - - + +
29A PHE* 6.3 1.3 - - + -
38A LEU* 4.1 16.6 - - + -
87A ASP 3.7 3.1 + - - +
88A ILE* 1.3 74.7 - - - +
90A THR* 1.3 62.5 + - - +
91A ILE* 3.5 29.6 - - + -
96A PHE* 2.8 48.7 + - + +
99A TYR* 3.9 20.0 - - + -
101A PHE* 4.5 6.1 - - + -
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Residues in contact with THR 90 (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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18A ALA* 3.5 2.4 - - - +
19A GLN* 2.8 59.2 + - - +
21A GLY 5.0 2.1 + - - -
24A LYS* 3.8 20.6 - - - +
88A ILE* 3.9 5.9 + - - +
89A VAL* 1.3 71.9 - - - +
91A ILE* 1.3 60.8 + - - +
93A ASN* 3.7 22.2 - - + +
94A LEU 3.1 23.6 - - - +
95A SER* 2.9 19.2 + - - +
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Residues in contact with ILE 91 (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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4A VAL* 4.3 13.5 - - + -
18A ALA* 3.8 21.8 - - + +
19A GLN* 4.8 0.2 - - - -
31A PHE* 4.4 17.3 - - + -
38A LEU* 4.7 9.6 - - + -
89A VAL* 3.5 30.5 - - + -
90A THR* 1.3 71.1 - - - +
92A ALA* 1.3 65.9 + - + +
94A LEU* 2.7 36.4 + - + +
96A PHE* 3.8 18.3 - - + -
121A VAL* 4.8 8.7 - - + -
136A VAL* 4.4 12.1 - - + -
165A LEU* 5.1 0.7 - - + -
167A ILE* 3.5 29.4 - - + -
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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