Contacts of the strand formed by residues 91 - 99 (chain A) in PDB entry 4GUP
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 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LEU* 3.9 13.0 - - + -
11A GLY 3.4 1.3 - - - -
12A VAL* 3.7 27.8 - - + -
77A LEU* 4.6 2.0 - - - -
90A HIS* 1.3 74.4 - - - +
92A TYR* 1.3 59.5 + - - +
93A GLN* 4.3 6.9 + - - -
113A ALA 3.8 0.3 - - - +
114A TYR* 3.4 6.9 - - - -
115A ASP* 2.8 36.4 + - - +
31B HIS* 3.3 35.7 - - + +
32B PRO* 4.8 9.6 - - + +
33B SER* 4.5 8.7 - - - +
62B PHE* 4.7 4.7 - - + -
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Residues in contact with TYR 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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10A LEU* 3.4 3.5 - - - +
11A GLY* 2.8 37.3 + - - +
73A PHE* 3.4 37.6 - + + -
76A GLU* 3.7 32.5 + - + +
77A LEU* 3.5 35.0 - - + -
80A LEU* 3.7 23.6 - - + +
91A THR* 1.3 74.2 - - - +
93A GLN* 1.4 60.5 + - - +
112A TYR* 3.1 40.3 - + + +
113A ALA 3.4 18.6 - - - -
114A TYR* 4.6 1.8 - - - -
119A PHE* 4.8 11.4 - + - -
139A ILE* 5.9 0.9 - - - +
143A TRP* 4.4 6.2 - - - -
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Residues in contact with GLN 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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9A ARG 3.3 4.7 - - - -
10A LEU* 3.7 17.9 - - + -
73A PHE* 4.2 2.5 - - - -
91A THR* 4.3 6.9 + - - -
92A TYR* 1.4 78.0 - - - +
94A ARG* 1.3 60.9 + - - +
112A TYR* 3.2 8.2 - - - +
113A ALA* 2.8 48.4 + - - +
116A GLY* 3.5 28.5 - - - +
31B HIS* 4.2 4.5 + - - -
56B PHE* 3.8 18.4 - - + -
60B TRP* 3.0 53.4 - - + +
62B PHE* 3.9 13.4 - - - -
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Residues in contact with ARG 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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7A TYR 5.3 1.3 + - - -
8A PHE* 3.3 8.0 - - - +
9A ARG* 3.0 60.1 + - + +
73A PHE* 3.8 18.2 - - + -
93A GLN* 1.3 74.9 - - - +
95A MET* 1.3 69.3 + - - +
96A ILE* 3.3 19.4 - - - +
110A LEU* 3.8 15.3 - - + +
111A GLN 3.4 7.6 - - - +
112A TYR* 3.4 39.8 + - + -
153A GLN* 3.7 17.0 + - - +
301A 6FP 3.1 32.1 + - - -
302A CL 3.6 23.2 - - - +
56B PHE* 3.6 1.9 - - - -
60B TRP* 4.5 1.1 - - - -
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Residues in contact with MET 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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6A ARG* 4.9 7.6 - - + -
7A TYR 3.7 9.4 - - - +
8A PHE* 4.7 7.4 - - + -
94A ARG* 1.3 78.5 - - - +
96A ILE* 1.4 71.2 + - - +
109A PHE* 3.6 27.5 - - + +
110A LEU* 3.2 8.8 + - - +
111A GLN* 2.9 67.8 + - + +
56B PHE* 4.4 14.6 - - + +
57B SER 5.6 1.3 - - - +
58B LYS* 3.8 26.7 - - + -
60B TRP* 4.3 15.7 - - + -
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Residues in contact with ILE 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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6A ARG* 3.4 4.2 - - - -
7A TYR* 3.2 48.4 + - + +
94A ARG* 3.3 26.7 - - - +
95A MET* 1.4 72.9 - - - +
97A GLY* 1.3 58.0 + - - +
109A PHE* 3.4 22.1 - - - +
110A LEU* 3.5 31.6 - - + -
153A GLN* 5.5 4.3 - - + +
156A TRP* 3.6 27.4 - - + -
157A LEU* 4.1 11.9 - - + -
301A 6FP 3.5 29.4 - - + +
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Residues in contact with GLY 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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5A LEU 2.9 16.8 - - - -
6A ARG* 4.0 1.8 - - - -
96A ILE* 1.3 80.3 - - - +
98A CYS* 1.3 61.3 + - - -
108A GLY* 3.4 1.9 - - - -
109A PHE* 2.9 37.6 + - - +
156A TRP* 3.9 5.7 - - - -
157A LEU* 3.7 3.5 - - - +
161A CYS* 4.1 11.4 - - - -
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Residues in contact with CYS 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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4A SER* 3.3 5.6 - - - -
5A LEU* 2.9 32.1 + - - +
97A GLY* 1.3 74.6 - - - +
99A GLU* 1.4 59.7 + - - +
107A THR 3.2 20.2 - - - +
108A GLY* 3.6 9.6 - - - +
109A PHE* 4.2 8.5 - - - -
157A LEU* 4.6 4.9 - - + +
161A CYS* 2.9 39.3 - - + -
162A ILE* 3.3 30.1 - - - -
165A LEU* 4.9 4.9 - - - +
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Residues in contact with GLU 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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2A THR* 4.3 10.3 - - - +
3A HIS 3.3 7.4 - - - +
4A SER* 3.6 22.2 - - - +
98A CYS* 1.4 73.1 - - - +
100A LEU* 1.3 60.5 + - - +
101A LEU* 3.4 24.4 - - + +
106A THR* 3.5 2.4 - - - -
107A THR* 3.3 39.2 + - - +
109A PHE* 5.4 8.7 - - + -
162A ILE* 3.4 13.8 - - - +
165A LEU* 4.7 0.9 - - - -
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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