Contacts of the strand formed by residues 85 - 95 (chain S) in PDB entry 2JA7
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 85 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175P PHE* 3.4 25.9 - - + -
179P GLN* 4.3 5.2 - - - +
1S MET* 2.7 39.9 - - + +
79S PHE* 4.7 2.1 - - - -
81S PRO* 3.4 4.6 - - - +
82S PHE* 3.1 49.1 + - + +
83S LYS 3.2 1.4 - - - -
84S GLY* 1.3 79.6 - - - +
86S VAL* 1.3 64.6 + - - +
87S VAL* 3.1 21.7 - - - +
146S LYS* 3.8 0.5 - - - -
147S ILE* 3.0 32.8 + - + +
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Residues in contact with VAL 86 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179P GLN* 2.7 27.0 + - - +
183P LEU* 3.8 20.9 - - + +
194P LEU* 2.9 50.1 + - + +
196P PRO* 5.6 0.4 - - + -
84S GLY 3.8 6.0 + - - +
85S GLU* 1.3 76.1 - - - +
87S VAL* 1.3 71.3 + - - +
144S ARG* 4.0 25.8 - - + -
145S VAL 3.6 11.4 - - - +
146S LYS* 4.6 15.7 - - + -
168S LEU* 4.5 2.0 - - + -
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Residues in contact with VAL 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P LEU* 6.2 1.6 - - + -
147P TYR* 4.5 4.7 - - - +
179P GLN* 4.8 4.3 - - - +
183P LEU* 5.0 1.6 - - + -
1S MET* 4.7 6.5 - - + -
79S PHE* 5.8 0.9 - - + -
85S GLU* 3.1 22.9 - - + +
86S VAL* 1.3 83.1 - - - +
88S ASP* 1.3 61.3 + - - +
103S VAL* 3.6 38.3 - - + +
108S VAL* 5.2 0.4 - - + -
144S ARG* 4.3 2.7 - - - -
145S VAL* 2.6 45.8 + - + +
147S ILE* 3.7 31.2 - - + -
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Residues in contact with ASP 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P LEU* 5.0 4.7 - - - +
147P TYR* 3.1 28.8 + - - -
151P PHE* 3.6 18.9 - - + +
182P SER 4.6 5.1 - - - +
183P LEU* 3.6 18.3 - - - +
87S VAL* 1.3 76.2 - - - +
89S GLY* 1.3 57.6 + - - +
103S VAL* 3.9 4.2 - - - +
143S ILE 3.1 17.9 - - - +
144S ARG* 3.5 32.7 + - + -
145S VAL 4.2 0.2 - - - +
171S ILE* 4.4 12.2 - - + +
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Residues in contact with GLY 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147P TYR* 4.1 1.6 - - - -
151P PHE* 3.5 16.4 - - - -
88S ASP* 1.3 75.0 - - - +
90S THR* 1.3 61.0 + - - -
91S VAL 3.9 0.2 + - - -
101S VAL* 3.5 21.2 - - - +
102S GLN 3.8 10.3 - - - -
103S VAL* 4.2 1.1 - - - -
142S ARG* 3.7 1.7 - - - -
143S ILE 2.9 31.1 + - - +
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Residues in contact with THR 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151P PHE* 3.1 24.6 - - - -
89S GLY* 1.3 73.4 - - - -
91S VAL* 1.3 74.0 + - - +
92S VAL* 3.6 1.5 - - + +
101S VAL* 4.2 0.7 - - - -
102S GLN* 2.7 41.0 + - - +
140S LYS* 3.5 33.7 - - + +
141S SER 4.2 2.7 - - - -
142S ARG* 4.6 6.5 + - + +
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Residues in contact with VAL 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90S THR* 1.3 85.1 - - - +
92S VAL* 1.3 68.4 + - - +
93S SER 3.7 15.9 - - - +
94S CYS* 4.6 2.2 - - + -
99S PHE* 3.8 14.1 - - + -
100S GLU 3.4 12.3 - - - +
101S VAL* 4.0 6.7 - - + +
137S ILE* 4.3 2.7 - - + -
138S THR 3.5 17.3 - - - +
139S ILE* 3.1 26.1 - - - +
141S SER* 3.1 22.1 + - - +
143S ILE* 3.4 31.2 - - + -
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Residues in contact with VAL 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90S THR* 3.6 2.2 - - - +
91S VAL* 1.3 82.6 - - - +
93S SER* 1.3 65.9 + - - +
94S CYS* 5.4 0.2 - - - +
100S GLU 2.8 14.5 + - - +
102S GLN* 3.5 40.4 - - + +
107S LYS* 4.0 26.2 - - + +
139S ILE* 4.3 20.5 - - - +
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Residues in contact with SER 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G GLN* 3.8 13.5 - - - -
97G HIS* 3.3 20.9 + - - -
91S VAL* 3.7 1.6 - - - +
92S VAL* 1.3 82.7 - - - +
94S CYS* 1.3 62.8 + - - +
99S PHE* 3.3 2.1 - - - +
100S GLU* 2.8 53.0 + - - +
107S LYS* 5.2 1.9 + - - -
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Residues in contact with CYS 94 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G GLN* 5.3 1.5 + - - -
97G HIS* 4.6 0.4 + - - -
91S VAL* 4.6 6.1 - - + -
92S VAL 5.4 0.2 - - - +
93S SER* 1.3 79.8 - - - +
95S SER* 1.3 60.6 + - - +
98S GLY 3.6 3.6 - - - -
99S PHE* 3.8 14.6 - - + +
121S PHE* 5.1 0.8 - - - -
128S PRO* 3.8 40.4 - - + +
129S SER* 4.6 3.6 - - - -
130S TYR* 3.3 40.8 - - - -
137S ILE* 4.9 3.4 - - - -
138S THR* 5.4 5.4 - - - -
139S ILE* 5.6 1.8 - - + +
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Residues in contact with SER 95 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G SER* 4.0 10.5 + - - -
96G GLN* 4.8 8.5 - - - -
97G HIS* 3.8 24.5 + - - -
93S SER 4.4 0.2 - - - -
94S CYS* 1.3 74.1 - - - +
96S GLN* 1.3 62.1 + - - +
97S HIS* 3.1 18.3 + - - +
98S GLY 2.7 17.2 + - - +
121S PHE* 3.5 9.7 - - - -
130S TYR* 2.8 34.5 + - - -
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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