Contacts of the strand formed by residues 88 - 98 (chain A) in PDB entry 4HJ5
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 TYR 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ALA 3.3 6.3 - - - -
22A GLN* 3.6 43.7 + - + -
83A ILE* 5.9 0.2 - - - +
86A GLY 4.0 9.9 - - - -
87A ASP* 1.3 78.1 - - - +
89A VAL* 1.3 55.9 + - - +
122A LYS* 3.4 8.9 - - - +
123A VAL* 2.7 36.7 + - + +
125A SER* 4.0 26.0 - - - -
130A LEU* 3.3 50.3 - - + -
133A ILE* 4.1 16.5 - - + +
134A LYS* 3.4 31.9 - - - +
137A LYS* 6.0 1.2 - - - +
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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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19A PHE 4.0 0.2 - - - +
20A TYR* 3.5 3.6 - - - +
21A ALA* 2.8 51.0 + - + +
23A VAL* 4.3 19.3 - - + -
35A LEU* 5.5 0.4 - - + -
37A VAL* 4.6 4.3 - - + -
83A ILE* 4.8 9.4 - - + -
88A TYR* 1.3 78.1 - - - +
90A VAL* 1.3 62.5 + - - +
91A MET* 4.0 21.1 - - + -
120A ILE* 3.1 40.8 - - + -
121A GLU 3.5 11.0 - - - +
122A LYS* 4.6 1.6 - - - +
123A VAL* 3.8 5.5 - - - +
130A LEU* 5.1 0.2 - - - +
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Residues in contact with VAL 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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5A PHE* 3.7 29.8 - - + -
19A PHE 3.5 4.9 - - - +
20A TYR* 3.8 15.3 - - + +
89A VAL* 1.3 73.0 - - - +
91A MET* 1.3 63.6 + - - +
92A LYS* 3.9 26.1 + - + +
119A SER* 3.9 1.9 + - - +
120A ILE* 3.4 3.5 - - - -
121A GLU* 2.9 49.9 + - + +
122A LYS 5.0 0.4 - - - +
123A VAL* 3.6 19.5 - - + +
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Residues in contact with MET 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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18A SER* 3.0 6.1 - - - -
19A PHE* 2.8 69.0 + - + +
35A LEU* 4.9 2.9 - - + -
37A VAL* 5.0 2.0 - - - -
69A CYS* 4.0 27.6 - - + -
71A LEU* 5.2 0.4 - - + -
89A VAL* 4.0 15.3 - - + -
90A VAL* 1.3 78.0 - - - +
92A LYS* 1.3 61.4 + - - +
94A VAL* 4.0 9.9 - - + -
106A CYS* 4.0 9.4 - - - -
108A LEU* 4.0 27.6 - - + -
119A SER 3.5 4.9 - - - +
120A ILE* 3.9 31.0 - - + -
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Residues in contact with LYS 92 (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 PHE* 4.2 15.9 - - + -
18A SER* 3.3 11.0 - - - +
20A TYR* 5.8 0.4 - - - -
90A VAL* 3.9 31.1 - - + +
91A MET* 1.3 76.2 - - - +
93A ASN* 1.3 75.1 + - - +
94A VAL* 3.1 6.5 + - - +
117A ASN 4.2 7.9 - - - +
118A MET* 3.3 0.3 - - - -
119A SER* 2.8 52.0 + - - +
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Residues in contact with ASN 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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16A ARG* 3.3 40.4 + - - +
17A CYS 2.9 11.1 + - - +
18A SER* 2.8 20.2 + - - -
92A LYS* 1.3 75.4 - - - +
94A VAL* 1.3 61.8 + - - +
116A TYR* 2.9 26.3 + - + +
117A ASN* 2.8 30.8 + - - +
118A MET* 3.6 15.8 - - - +
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Residues in contact with VAL 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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15A GLN 3.7 0.5 - - - +
16A ARG* 3.4 5.1 - - - -
17A CYS* 2.9 38.1 + - - +
19A PHE* 3.9 20.9 - - + -
91A MET* 4.0 22.4 - - + +
92A LYS 3.6 12.6 - - - +
93A ASN* 1.3 78.7 - - - +
95A ARG* 1.3 61.4 + - - +
106A CYS* 3.6 24.0 - - - -
108A LEU* 3.7 22.0 - - + -
118A MET* 3.9 13.7 - - + -
119A SER 4.1 4.7 - - - +
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Residues in contact with ARG 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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14A HIS* 3.0 47.0 + - - +
15A GLN* 3.9 12.7 - - - +
16A ARG* 4.1 6.4 - - - +
93A ASN 4.1 0.6 + - - -
94A VAL* 1.3 76.5 - - - +
96A THR* 1.3 77.6 + - - +
97A LYS* 5.8 4.9 - - + -
106A CYS* 3.4 8.3 - - - -
107A ILE* 3.1 43.0 + - + +
109A HIS* 5.5 10.1 - - + +
118A MET* 4.5 5.3 - - - -
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Residues in contact with THR 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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11A ILE* 4.3 16.2 - - + -
12A THR 2.8 21.7 + - - +
14A HIS* 3.0 28.8 + - - -
15A GLN 3.3 8.8 + - - +
17A CYS* 3.7 29.4 - - - -
19A PHE* 5.9 0.2 - - + -
95A ARG* 1.3 92.6 + - - +
97A LYS* 1.3 63.1 + - - +
104A LEU* 3.8 11.7 - - + -
105A GLU 3.3 11.7 - - - +
106A CYS* 4.6 8.5 - - + -
107A ILE* 5.8 0.7 - - - -
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Residues in contact with LYS 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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13A PRO* 4.6 0.2 - - - -
14A HIS* 4.2 15.3 - - + +
95A ARG* 5.8 4.7 - - + -
96A THR* 1.3 75.9 - - - +
98A ILE* 1.3 78.3 + - - +
99A ASP* 4.6 2.5 - - - +
104A LEU* 3.0 11.3 - - - +
105A GLU* 3.0 36.8 + - - +
107A ILE* 3.7 27.5 - - + +
109A HIS* 4.3 19.2 + - - -
1B G 5.9 1.0 - - - -
2B G 4.1 21.5 + - - +
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Residues in contact with ILE 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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13A PRO* 3.4 24.2 - - + -
14A HIS* 3.0 35.3 - - + +
45A LEU* 5.4 3.4 - - + -
97A LYS* 1.3 90.4 - - - +
99A ASP* 1.3 64.9 + - - +
102A GLY* 3.2 42.6 - - - +
103A TYR 3.2 5.6 - - - +
104A LEU* 4.8 1.8 - - + -
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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