Contacts of the strand formed by residues 57 - 65 (chain S) in PDB entry 1ESV
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 LEU 57 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S GLY 3.6 13.5 - - - +
13S LYS* 4.0 11.9 - - - +
14S GLU* 4.6 0.4 - - - -
15S PRO* 4.1 26.5 - - + -
49S THR* 3.6 25.1 - - + -
50S VAL 3.7 5.6 - - - +
51S GLN* 4.4 10.3 - - - +
52S LEU* 3.5 4.3 - - - -
55S GLY 4.9 2.0 - - - +
56S ASN* 1.3 94.6 + - - +
58S GLN* 1.3 60.1 + - - +
59S TYR* 3.4 26.7 - - + +
91S ARG* 2.5 34.7 + - - +
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Residues in contact with GLN 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48S LYS* 3.3 2.5 + - - +
49S THR* 3.2 6.9 - - - -
50S VAL* 2.9 67.6 + - + +
52S LEU* 3.6 27.5 - - + +
57S LEU* 1.3 72.7 - - - +
59S TYR* 1.3 64.7 + - - +
60S ASP* 3.7 21.4 + - - +
93S VAL* 6.3 1.3 - - + -
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Residues in contact with TYR 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S GLY* 2.8 31.9 + - - -
47S LEU* 3.7 16.4 - - + -
48S LYS 3.5 1.6 - - - -
49S THR* 3.1 35.9 - - + -
56S ASN* 5.1 0.2 + - - -
57S LEU* 3.4 21.7 - - + +
58S GLN* 1.3 76.5 - - - +
60S ASP* 1.3 69.8 + - - +
88S LEU* 3.9 32.2 - - + +
91S ARG* 3.7 47.1 + - + +
92S ALA* 3.5 15.9 - - + -
93S VAL* 3.1 23.1 + - - +
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Residues in contact with ASP 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46S ILE 3.4 4.2 - - - +
47S LEU* 3.4 4.0 - - - -
48S LYS* 3.0 36.8 + - + +
58S GLN* 3.7 24.6 + - - +
59S TYR* 1.3 79.7 - - - +
61S LEU* 1.3 60.1 + - - +
62S HIS* 3.7 21.0 - - - +
93S VAL* 3.3 17.3 - - - +
95S HIS* 2.7 25.2 + - - +
105S THR* 5.8 2.9 - - - +
109S TYR* 3.7 11.3 + - - +
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Residues in contact with LEU 61 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45S VAL* 4.1 14.4 - - + -
46S ILE 3.3 3.6 - - - +
47S LEU* 4.0 23.6 - - + -
59S TYR 4.2 0.2 - - - -
60S ASP* 1.3 73.7 - - - +
62S HIS* 1.3 55.3 - - - +
81S THR* 3.7 26.3 - - + +
84S LEU* 3.4 34.3 - - + -
85S ASP* 3.6 26.9 - - + +
88S LEU* 4.9 1.6 - - + -
92S ALA* 3.4 26.2 - - + -
93S VAL 2.7 14.3 + - - +
94S GLN* 3.3 1.7 - - + -
95S HIS* 2.7 33.6 + - - -
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Residues in contact with HIS 62 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45S VAL* 3.4 2.3 - - - +
46S ILE* 2.5 48.0 + - + +
60S ASP* 3.7 11.8 - - - +
61S LEU* 1.3 76.9 - - - +
63S TYR* 1.3 60.2 + - - +
64S TRP 3.9 0.2 - - - -
81S THR* 4.7 2.2 - - - -
95S HIS* 3.1 36.5 - + - +
97S GLU* 2.6 34.9 + - + -
103S SER* 4.2 3.6 - - - -
105S THR* 4.6 3.8 - - + -
106S PHE* 3.4 35.1 - + + -
109S TYR* 2.8 40.9 + + - -
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Residues in contact with TYR 63 (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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146A GLY 3.5 22.2 - - - -
147A ARG* 3.8 2.3 - - - -
148A THR* 3.1 43.5 + - + -
149A THR* 4.6 1.0 + - - -
44S TYR 3.3 9.4 - - - +
45S VAL* 4.4 0.9 - - + +
62S HIS* 1.3 72.1 - - - +
64S TRP* 1.3 61.5 + - - +
65S LEU* 4.0 12.1 + - + +
77S ALA* 3.8 15.5 - - + +
78S ALA* 3.8 20.2 - - + -
81S THR* 3.6 31.9 - - + +
94S GLN* 4.9 1.3 - - + -
95S HIS 2.9 29.8 + - - -
96S ARG* 3.5 26.8 + - + +
97S GLU* 2.8 25.6 + - - +
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Residues in contact with TRP 64 (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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38S PHE* 3.6 33.7 - + + -
39S PHE 3.4 21.8 - - - -
40S THR* 4.2 7.2 - - - -
42S ASP 3.7 2.9 - - - -
43S ALA* 3.3 5.5 - - - +
44S TYR* 2.9 50.8 + + + +
46S ILE* 4.0 20.2 - - + -
62S HIS 3.9 0.8 + - - -
63S TYR* 1.3 73.9 - - - +
65S LEU* 1.3 60.2 + - - +
66S GLY* 3.4 25.4 - - - -
97S GLU* 3.3 15.9 - - + -
99S GLN* 3.7 23.5 - - + +
102S GLU* 2.9 38.7 + - + +
106S PHE* 3.9 16.7 - + + -
114S LEU* 5.0 0.4 - - - +
116S TYR* 3.8 18.8 - + - -
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Residues in contact with LEU 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLY* 3.9 10.8 - - - +
42S ASP 4.2 2.0 - - - -
43S ALA* 3.7 9.0 - - + -
63S TYR* 4.3 10.3 - - + +
64S TRP* 1.3 84.5 - - - +
66S GLY* 1.3 63.1 + - - +
69S CYS* 4.1 9.4 - - - -
74S SER* 3.5 41.1 - - - +
77S ALA* 4.2 8.7 - - + -
96S ARG* 3.9 40.6 - - + +
97S GLU 2.9 13.7 + - - +
98S VAL* 4.0 10.1 - - + +
99S GLN 3.1 22.3 + - - -
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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