Contacts of the strand formed by residues 94 - 102 (chain A) in PDB entry 4QMG
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 GLU 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ARG* 3.5 22.1 + - + +
22A GLY 3.6 12.6 - - - +
23A ILE* 4.5 10.8 - - + -
92A GLY 4.0 1.2 + - - -
93A LYS* 1.3 76.6 - - - +
95A VAL* 1.3 70.7 + - - +
114A LEU* 4.4 2.4 - - - +
115A GLY* 3.6 21.1 + - - +
116A LYS* 3.7 37.5 - - - +
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Residues in contact with VAL 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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21A ARG* 3.7 5.2 - - - +
22A GLY 3.0 43.6 + - - +
24A ILE* 3.6 41.3 - - + -
35A VAL* 4.4 9.9 - - + -
90A LEU* 4.1 16.8 - - + -
93A LYS 4.3 1.1 - - - +
94A GLU* 1.3 79.5 - - - +
96A CYS* 1.3 60.8 + - - +
97A PHE* 4.5 5.6 - - + -
112A ILE* 4.1 14.8 - - + -
113A TYR 3.2 14.4 - - - +
114A LEU* 4.1 7.6 - - + -
115A GLY 3.8 6.1 - - - -
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Residues in contact with CYS 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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19A VAL* 4.0 8.5 - - + -
20A GLN 3.4 10.8 - - - +
21A ARG* 3.9 24.0 - - - +
95A VAL* 1.3 75.2 - - - +
97A PHE* 1.3 63.6 + - - +
112A ILE* 3.8 0.3 - - - -
113A TYR* 2.8 50.3 + - - +
115A GLY 3.7 4.5 + - - +
116A LYS 4.0 1.6 - - - +
117A ASP 3.3 40.2 - - - -
118A THR* 3.9 2.5 - - - -
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Residues in contact with PHE 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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19A VAL* 4.9 0.6 - - - +
20A GLN* 2.9 62.3 + - + +
21A ARG 3.2 30.7 - - - -
35A VAL* 3.9 22.7 - - + -
47A ARG* 3.8 27.8 - - + -
49A ILE* 3.4 29.4 - - + -
95A VAL* 4.5 5.6 - - + -
96A CYS* 1.3 79.0 - - - +
98A THR* 1.3 63.9 + - - +
99A ILE* 3.9 11.4 - - + -
111A MSE 3.2 15.7 - - - +
112A ILE* 4.2 14.1 - - + -
113A TYR* 4.6 2.2 - - - -
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Residues in contact with THR 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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17A PRO* 4.2 18.4 - - + +
18A THR 3.5 21.8 - - - +
19A VAL* 3.5 19.3 - - + +
20A GLN* 5.1 0.2 - - - -
49A ILE* 5.7 0.2 - - - +
97A PHE* 1.3 76.2 - - - +
99A ILE* 1.3 65.8 + - - +
110A GLY* 3.2 2.8 - - - -
111A MSE 3.0 54.8 + - - +
113A TYR* 4.3 11.5 + - + -
118A THR* 5.4 5.4 - - - +
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Residues in contact with ILE 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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17A PRO* 4.8 11.4 - - - +
18A THR 4.6 2.7 + - - +
20A GLN* 3.5 21.5 + - - +
47A ARG* 4.0 5.6 - - - +
49A ILE* 4.4 20.4 - - + -
97A PHE* 3.9 20.6 - - + -
98A THR* 1.3 75.2 - - - +
100A GLU* 1.3 62.5 + - - +
101A ASN 3.5 18.6 - - - +
102A LYS* 4.9 4.9 - - + -
108A GLU* 3.7 33.7 - - + +
109A TYR 3.5 11.4 - - - +
111A MSE 4.9 0.7 - - - -
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Residues in contact with GLU 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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52A SER* 3.4 23.9 + - - +
53A ASN* 4.3 17.8 + - - +
98A THR 3.7 2.2 + - - -
99A ILE* 1.3 74.5 - - - +
101A ASN* 1.3 66.0 - - + +
109A TYR* 2.7 14.1 + - - +
111A MSE 3.8 23.8 - - + +
143A ASN* 5.1 7.4 + - - -
145A GLU* 5.5 1.7 - - - +
146A GLN* 5.6 0.2 + - - -
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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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99A ILE* 3.5 7.7 - - - +
100A GLU* 1.3 89.1 - - + +
102A LYS* 1.3 83.1 + - - +
103A THR* 3.8 17.4 + - - +
107A ARG 4.6 0.2 - - - -
108A GLU* 3.6 0.3 - - - -
109A TYR* 2.7 46.8 + - + +
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Residues in contact with LYS 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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99A ILE* 4.9 5.4 - - + -
101A ASN* 1.3 90.3 + - - +
103A THR* 1.3 71.0 + - - +
104A PRO* 3.7 2.4 - - - +
106A GLY* 3.9 15.6 + - - +
107A ARG 3.3 5.6 - - - +
108A GLU* 3.7 37.4 + - + +
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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