Contacts of the strand formed by residues 87 - 98 (chain A) in PDB entry 5J6Y
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 ASP 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLY* 3.4 3.1 - - - -
24A THR* 2.9 36.8 + - + +
26A SER 3.2 19.5 - - - +
27A GLN* 3.0 1.7 - - - +
28A LEU* 3.0 26.6 + - + -
62A ALA* 3.5 10.2 - - - +
86A THR* 1.3 100.0 + - - +
88A GLY* 1.3 58.2 + - - +
155A ASP* 3.5 8.7 - - - +
156A GLN* 3.2 13.8 - - - +
302A CA 2.4 31.6 - - - -
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Residues in contact with GLY 88 (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 TYR* 4.0 13.5 - - - -
22A TYR 3.1 13.2 - - - -
23A GLY* 4.0 0.4 - - - -
24A THR 4.7 0.2 - - - -
28A LEU* 3.9 10.5 - - - +
61A VAL* 4.0 7.1 - - - +
62A ALA* 4.1 3.4 - - - +
87A ASP* 1.3 76.3 - - - +
89A GLY* 1.3 58.5 + - - -
154A TRP* 3.4 1.2 - - - +
155A ASP* 2.8 34.7 + - - +
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Residues in contact with GLY 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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21A TYR* 3.2 10.5 - - - -
22A TYR 2.9 31.7 + - - -
34A PHE* 3.3 15.8 - - - -
88A GLY* 1.3 74.6 - - - -
90A ILE* 1.3 63.9 + - - -
153A TRP* 3.1 21.5 - - - -
154A TRP* 3.8 2.0 - - - -
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Residues in contact with ILE 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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20A GLU 3.2 9.0 - - - +
21A TYR* 4.3 10.3 - - + -
34A PHE* 3.3 8.0 - - - -
47A PHE* 4.0 22.2 - - + -
54A TYR* 3.9 33.9 - - + -
67A LEU* 4.8 5.2 - - + -
70A PHE* 4.5 7.4 - - + -
71A LEU* 4.9 0.2 - - + -
89A GLY* 1.3 79.3 - - - +
91A TYR* 1.3 59.5 + - - +
92A LEU* 4.1 22.4 - - + -
151A MET* 6.2 0.2 - - + -
152A ILE* 3.2 5.8 - - - -
153A TRP* 2.9 60.5 + - + +
162A PHE* 4.4 9.9 - - + -
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Residues in contact with TYR 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 VAL 3.6 2.4 - - - +
19A GLY* 3.6 0.2 - - - -
20A GLU* 2.9 62.6 + - + +
22A TYR* 4.7 0.7 - - + -
34A PHE* 4.3 0.2 - - - -
35A ARG* 5.4 4.7 - - - -
38A VAL* 4.2 29.6 - - + -
90A ILE* 1.3 73.4 - - - +
92A LEU* 1.3 74.2 + - - +
93A GLN* 3.7 27.5 - - + +
150A ASP* 4.1 17.4 + - + +
151A MET 3.3 10.3 - - - -
152A ILE* 3.9 17.3 - - + -
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Residues in contact with LEU 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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17A LEU* 3.9 14.8 - - + -
18A VAL 3.2 3.8 - - - +
19A GLY* 3.7 18.2 - - - -
47A PHE* 3.7 19.7 - - + -
49A ALA* 3.9 12.8 - - + -
52A ILE* 3.9 34.5 - - + -
54A TYR* 4.6 1.6 - - + -
90A ILE* 4.1 22.0 - - + -
91A TYR* 1.3 82.5 - - - +
93A GLN* 1.3 60.3 + - - +
150A ASP* 3.1 7.0 - - - +
151A MET* 2.8 55.4 + - + +
162A PHE* 4.9 0.7 - - + -
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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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17A LEU* 4.0 5.1 - - - +
18A VAL* 2.8 63.8 + - + +
91A TYR* 3.7 32.8 - - + +
92A LEU* 1.3 77.4 - - - +
94A GLY* 1.3 64.9 + - - +
95A TYR* 5.6 2.1 - - - -
149A ILE 3.5 5.6 - - - +
150A ASP* 4.0 8.5 - - + -
184A SER 4.9 2.6 + - - +
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Residues in contact with GLY 94 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.6 9.5 - - - +
93A GLN* 1.3 83.2 + - - +
95A TYR* 1.3 81.2 + - - -
148A ALA* 3.6 3.5 - - - +
149A ILE* 2.9 27.3 + - - +
183A SER 3.9 4.0 - - - -
184A SER* 3.9 7.2 - - - -
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Residues in contact with TYR 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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4A ALA 3.6 19.3 + - - -
17A LEU* 3.5 8.0 - - - +
93A GLN* 5.6 2.0 - - - -
94A GLY* 1.3 83.9 - - - -
96A VAL* 1.3 61.6 + - - +
146A TYR* 4.0 25.6 - - + -
147A GLN 3.1 19.5 - - - +
148A ALA* 3.8 18.7 - - + +
149A ILE* 3.9 3.4 - - - -
182A LEU* 3.4 4.7 - - - -
183A SER 2.9 35.8 + - - +
184A SER 3.9 3.6 - - - -
185A THR* 3.4 22.2 - - - -
186A GLY* 3.3 26.2 - - - -
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A TYR* 1.3 75.3 - - - +
97A TYR* 1.3 68.6 + - - +
98A LEU* 3.3 25.1 + - + -
117A ILE* 4.8 3.1 - - + -
146A TYR* 3.9 2.5 - - - -
147A GLN* 2.8 45.1 + - + +
149A ILE* 3.9 27.1 - - + -
166A LEU* 5.6 0.4 - - + -
177A LEU* 4.2 9.6 - - + -
181A ILE* 3.5 36.1 - - + +
182A LEU* 4.0 13.2 - - + -
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Residues in contact with TYR 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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96A VAL* 1.3 70.2 - - - +
98A LEU* 1.3 81.5 + - - +
99A GLU* 4.3 16.2 - - + +
144A SER* 4.5 8.0 - - - -
145A GLY* 3.5 34.5 + - - -
146A TYR* 3.6 31.9 - + + +
181A ILE* 2.8 44.1 + - + +
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Residues in contact with LEU 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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96A VAL* 3.3 25.5 + - + +
97A TYR* 1.3 85.9 - - - +
99A GLU* 1.3 64.2 + - - +
103A TYR* 3.7 32.3 - - + +
117A ILE* 4.4 13.2 - - + -
139A PHE* 4.8 0.7 - - + -
141A ILE* 4.0 22.9 - - + -
145A GLY 3.0 30.5 + - - +
147A GLN* 3.4 22.0 + - + -
166A LEU* 3.9 22.7 - - + -
175A PHE* 4.9 3.6 - - + -
181A ILE* 4.7 5.4 - - + -
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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