Contacts of the strand formed by residues 77 - 84 (chain A) in PDB entry 1Q21
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 GLY 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LYS 3.3 3.8 + - - -
6A LEU* 3.3 5.5 - - - +
7A VAL* 2.8 25.6 + - - +
75A GLY 3.3 2.0 - - - -
76A GLU* 1.3 82.3 - - - +
78A PHE* 1.4 68.5 + - - -
110A PRO 3.3 11.2 - - - -
159A LEU* 3.8 8.1 - - - -
163A ILE* 3.9 15.9 - - - +
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Residues in contact with PHE 78 (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 VAL* 3.2 37.7 - - + +
9A VAL* 4.7 2.7 - - + -
72A MET* 3.4 43.5 - - + -
75A GLY* 3.9 22.0 - - - -
77A GLY* 1.4 79.1 - - - -
79A LEU* 1.3 61.1 + - - +
80A CYS* 3.9 2.7 - - - -
100A ILE* 3.8 39.5 - - + -
103A VAL* 5.7 0.4 - - + -
104A LYS* 4.2 5.6 - - + -
109A VAL* 3.6 33.4 - - + -
110A PRO 2.9 9.8 + - - +
111A MET* 3.1 12.1 - - + +
112A VAL 3.0 24.8 + - - -
159A LEU* 3.7 6.4 - - - +
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Residues in contact with LEU 79 (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 LEU* 6.3 0.2 - - + -
7A VAL 2.8 12.0 + - - +
8A VAL* 3.5 17.8 - - + -
9A VAL* 2.8 31.2 + - - +
19A LEU* 4.9 5.8 - - + -
78A PHE* 1.3 71.9 - - - +
80A CYS* 1.4 57.6 + - - +
81A VAL* 3.7 5.6 + - + +
112A VAL* 3.7 12.6 - - + -
114A VAL* 3.6 23.3 - - + -
155A ALA* 3.9 17.3 - - + +
156A PHE* 3.8 40.8 - - + -
159A LEU* 3.5 34.9 - - + +
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Residues in contact with CYS 80 (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 VAL* 3.7 12.6 - - + -
78A PHE* 4.6 1.3 - - - -
79A LEU* 1.4 70.2 - - - +
81A VAL* 1.3 61.7 + - - +
93A ILE* 4.2 17.5 - - + -
96A TYR* 5.0 4.9 - - - -
97A ARG* 5.3 3.4 - - - -
100A ILE* 4.1 19.5 - - - -
111A MET* 3.9 31.6 - - - -
112A VAL 2.9 15.5 + - - +
113A LEU* 3.5 19.2 - - + +
114A VAL 2.7 25.6 + - - -
139A ILE* 5.8 2.2 - - + -
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Residues in contact with VAL 81 (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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8A VAL* 3.6 25.4 - - + -
9A VAL 3.0 16.3 + - - +
10A GLY* 3.6 20.1 - - - -
11A ALA 4.2 1.0 + - - -
14A VAL* 3.7 27.0 - - + +
16A LYS* 4.4 5.4 - - + +
19A LEU* 4.0 25.6 - - + -
79A LEU* 3.8 7.0 - - + +
80A CYS* 1.3 77.3 - - - +
82A PHE* 1.4 71.3 + - - +
89A SER 5.0 0.5 - - - +
93A ILE* 4.0 6.3 - - - +
114A VAL* 3.3 16.8 - - + +
116A ASN* 4.0 10.5 - - + -
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Residues in contact with PHE 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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14A VAL* 3.9 9.2 - - - -
81A VAL* 1.4 76.8 - - - +
83A ALA* 1.3 76.9 + - - +
84A ILE* 3.7 18.4 - - + -
89A SER* 3.4 17.9 - - - +
90A PHE* 3.7 51.4 - + + +
93A ILE* 4.1 3.6 - - + -
113A LEU* 3.9 20.6 - - + -
114A VAL 2.9 16.9 + - - +
115A GLY* 3.6 20.9 - - - -
116A ASN* 2.8 25.3 + - - +
125A VAL* 4.0 13.2 - - + -
130A ALA* 4.2 0.9 - - + -
141A TYR* 3.8 25.8 - + - -
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Residues in contact with ALA 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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13A GLY 4.9 0.4 - - - +
14A VAL* 3.9 14.8 - - + +
82A PHE* 1.3 86.0 - - - +
84A ILE* 1.3 58.7 + - - +
85A ASN* 2.8 28.7 + - - +
86A ASN* 3.1 22.7 + - + +
89A SER* 3.1 8.7 + - - +
116A ASN 3.4 8.1 - - - +
117A LYS* 4.2 20.0 - - + +
125A VAL* 4.4 0.7 - - - +
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Residues in contact with ILE 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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82A PHE* 3.7 11.2 - - + -
83A ALA* 1.3 71.2 - - - +
85A ASN* 1.3 62.3 + - + +
86A ASN 3.6 0.4 - - - -
115A GLY* 3.5 26.0 - - - +
116A ASN 2.8 12.5 + - - +
117A LYS* 3.9 22.9 - - + +
118A CYS* 4.3 5.6 - - + -
120A LEU* 4.5 8.1 - - + +
123A ARG* 2.9 48.7 - - + +
124A THR* 2.9 21.0 + - - -
125A VAL* 3.0 16.2 + - + +
141A TYR* 3.5 11.9 - - - +
143A GLU* 3.3 20.0 - - - +
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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