Contacts of the strand formed by residues 100 - 109 (chain A) in PDB entry 4PSQ
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A LYS* 3.5 8.3 - - - +
90A TYR* 2.7 53.8 + - - -
99A LYS* 1.3 75.4 - - - +
101A ASN* 1.3 62.5 + - - +
201A 2WL 3.7 12.4 - - - -
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Residues in contact with ASN 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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87A LYS* 3.7 36.0 + - - +
88A MET 3.3 15.9 + - - +
89A LYS* 3.9 22.4 - - + +
90A TYR* 3.4 3.8 + - - -
100A GLY* 1.3 74.3 - - - +
102A ASP* 1.3 66.2 + - - +
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Residues in contact with ASP 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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87A LYS* 3.6 8.0 - - - +
88A MET* 2.7 46.1 + - + +
90A TYR* 3.3 20.1 + - + -
101A ASN* 1.3 78.4 + - - +
103A ASP* 1.3 70.2 + - - +
119A SER* 3.8 2.7 - - - +
121A ARG* 2.9 53.1 + - - +
133A TYR* 2.9 21.5 + - - +
201A 2WL 4.3 0.3 - - - -
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Residues in contact with ASP 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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6A VAL* 6.1 0.2 - - - +
86A PHE 3.6 5.9 - - - +
87A LYS* 3.1 33.2 + - - +
102A ASP* 1.3 76.8 - - - +
104A HIS* 1.3 59.6 + - - +
105A TRP* 4.0 28.4 + - + +
118A TYR 4.5 0.2 - - - -
119A SER* 2.7 37.0 + - - +
120A CYS* 3.6 20.2 + - - +
133A TYR* 4.4 1.4 + - - -
204A EDO 3.1 27.6 + - - -
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Residues in contact with HIS 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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45A PHE* 4.0 18.4 - + - -
53A MET* 5.2 1.3 - - + -
77A PHE* 3.4 42.1 - + + -
86A PHE* 2.9 43.8 + + - +
88A MET* 3.7 22.4 - - + +
102A ASP 3.7 0.2 + - - -
103A ASP* 1.3 73.4 + - - +
105A TRP* 1.3 62.1 + - - +
106A ILE* 3.7 29.3 - - + +
117A GLN* 3.7 25.6 + - + +
118A TYR 3.9 2.5 - - - -
137A PHE* 5.6 1.8 - + - -
201A 2WL 4.0 17.0 - - + +
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Residues in contact with TRP 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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6A VAL* 3.4 45.1 - - + -
9A PHE* 4.2 17.3 - + + -
11A VAL* 3.9 21.3 - - + -
84A ALA 3.5 3.6 - - - -
85A LYS* 3.5 47.5 - - + +
86A PHE 4.3 2.5 + - - -
103A ASP* 4.0 23.6 - - + +
104A HIS* 1.3 88.3 - - - +
106A ILE* 1.3 61.3 + - - +
107A VAL* 3.3 5.8 + - + -
117A GLN* 3.3 4.3 - - - +
118A TYR* 2.9 60.5 + + + +
119A SER* 6.0 0.2 - - - -
120A CYS* 6.2 1.3 - - + -
211A EDO 3.5 26.2 - - - -
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Residues in contact with ILE 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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11A VAL* 3.7 1.9 - - - +
12A LYS* 3.0 24.8 + - + +
15A PHE* 3.7 47.1 - - + -
20A PHE* 3.7 28.5 - - + -
45A PHE* 5.3 0.9 - - + -
53A MET* 5.5 1.1 - - + -
84A ALA* 3.0 19.5 + - - +
86A PHE* 4.7 3.8 - - + -
104A HIS* 3.7 28.0 - - + +
105A TRP* 1.3 69.9 - - - +
107A VAL* 1.3 59.1 + - - +
108A ASP 4.0 10.8 - - - +
109A THR* 4.0 18.2 - - + -
115A ALA* 5.2 0.7 - - + -
116A VAL 3.8 3.4 - - - +
117A GLN* 4.6 9.0 - - + +
137A PHE* 6.1 0.2 - - + -
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Residues in contact with VAL 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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10A ARG 3.6 3.8 - - - +
11A VAL* 3.3 9.2 - - + +
12A LYS 3.2 14.3 + - - -
105A TRP* 3.9 9.2 - - + +
106A ILE* 1.3 72.6 - - - +
108A ASP* 1.3 62.1 + - - +
116A VAL* 2.8 20.7 + - + +
117A GLN 4.1 1.3 - - - -
118A TYR* 3.3 34.5 - - + +
155A ARG* 4.1 12.8 - - + -
159A LEU* 4.2 17.5 - - + -
205A EDO 3.2 34.1 - - - +
213A EDO 3.2 12.1 - - - -
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Residues in contact with ASP 108 (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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12A LYS* 3.8 18.5 + - - +
106A ILE* 3.4 3.8 - - - +
107A VAL* 1.3 80.7 - - - +
109A THR* 1.3 85.9 + - - +
114A TYR* 3.1 23.8 + - + +
115A ALA* 4.0 0.5 - - - +
116A VAL* 2.9 29.9 + - + +
151A ILE* 4.0 0.9 - - - +
155A ARG* 2.6 45.8 + - + -
213A EDO 3.6 13.7 - - - -
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Residues in contact with THR 109 (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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12A LYS* 2.9 33.4 + - + +
15A PHE* 4.4 0.4 - - + -
20A PHE* 3.8 7.0 - - + -
24A TRP* 3.7 2.9 - - - -
106A ILE* 4.0 14.8 - - + -
108A ASP* 1.3 87.5 + - - +
110A ASP* 1.3 62.4 + - - +
111A TYR* 3.0 43.6 + - + -
114A TYR* 2.7 34.8 + - - -
115A ALA* 3.5 11.4 - - - +
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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