Contacts of the strand formed by residues 111 - 120 (chain A) in PDB entry 3B7C
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 ARG 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LEU* 5.0 3.8 - - - +
27A GLN* 2.9 47.6 + - - +
28A GLY* 5.0 1.0 - - - -
29A TYR 5.0 3.2 + - - -
31A GLN 6.2 0.2 - - - +
106A GLU 3.4 0.9 - - - +
107A LYS* 4.2 2.7 - - - -
108A ILE 2.9 31.7 + - - +
109A ASP* 3.0 6.0 + - + +
110A ASP* 1.3 79.8 - - - +
112A TRP* 1.3 74.9 + - - +
113A VAL* 3.5 23.2 + - + +
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Residues in contact with TRP 112 (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 PRO* 3.7 32.1 - - + +
5A ASP* 3.7 36.3 + - + +
6A ILE* 4.0 19.1 - - + -
9A LEU* 3.4 26.7 - - + +
76A MSE 3.9 13.5 - - + -
79A ASN 3.5 25.8 - - - -
80A TYR* 3.6 6.5 - - - -
81A ALA* 3.6 28.7 - - - -
82A ALA 4.2 0.9 - - - -
105A VAL* 3.9 20.0 - - + -
106A GLU* 3.5 22.2 - - - -
107A LYS* 3.7 22.7 - - + +
110A ASP 6.2 0.2 - - - -
111A ARG* 1.3 81.6 + - - +
113A VAL* 1.3 64.5 + - - +
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Residues in contact with VAL 113 (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 LEU* 4.5 0.7 - - - -
27A GLN 4.5 4.3 - - - +
28A GLY 3.6 4.7 - - - +
29A TYR 4.5 1.1 - - - +
30A TRP* 3.7 37.7 - - + +
105A VAL* 3.2 4.6 - - - -
106A GLU 2.9 38.5 + - - +
108A ILE* 3.9 26.7 - - + +
111A ARG* 3.6 40.2 - - + +
112A TRP* 1.3 80.3 - - - +
114A ILE* 1.3 62.6 + - - +
115A THR* 3.4 1.6 + - + +
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Residues in contact with ILE 114 (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 LEU* 4.0 6.7 - - + -
10A LEU* 4.3 4.9 - - + -
13A GLN* 3.6 25.6 - - - +
28A GLY 2.9 21.7 + - - +
29A TYR* 3.5 26.0 - - + -
30A TRP 2.9 24.1 + - - -
35A LEU* 3.2 8.9 - - + +
103A LEU* 4.0 12.1 - - + -
104A LEU 3.5 6.1 - - - +
105A VAL* 3.8 17.5 - - + -
113A VAL* 1.3 69.7 - - - +
115A THR* 1.3 62.6 + - - +
116A MSE 3.5 22.4 - - - +
117A ASP* 3.9 8.7 - - + -
128A EDO 3.6 18.4 - - - -
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Residues in contact with THR 115 (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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30A TRP* 3.7 30.1 - - + -
34A GLN 4.5 0.9 - - - +
35A LEU* 3.6 11.9 - - - +
36A MSE 3.2 22.0 + - - +
104A LEU* 2.9 23.1 + - - +
106A GLU* 2.8 31.9 + - + +
108A ILE* 3.8 21.5 - - + -
113A VAL 3.4 9.8 + - - +
114A ILE* 1.3 76.7 - - - +
116A MSE 1.3 62.7 + - - +
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Residues in contact with MSE 116 (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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36A MSE 3.2 24.9 - - + +
37A LEU* 5.5 0.2 - - - -
38A ILE* 3.5 21.8 - - + -
102A THR* 3.8 12.1 - - - +
103A LEU* 3.3 4.0 - - - -
104A LEU* 2.9 49.4 + - + +
114A ILE* 3.5 5.9 - - - +
115A THR* 1.3 84.1 + - - +
117A ASP* 1.3 65.5 + - - +
118A HIS* 3.7 22.0 - - + +
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Residues in contact with ASP 117 (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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29A TYR* 3.0 23.5 + - + -
36A MSE 2.9 7.9 + - - -
37A LEU* 3.3 23.2 - - + +
38A ILE* 2.8 32.9 + - - +
102A THR 3.7 2.9 - - - -
103A LEU* 3.3 19.9 - - + +
114A ILE* 3.9 9.0 - - + -
116A MSE 1.3 76.2 - - - +
118A HIS* 1.3 56.1 + - - +
119A SER* 2.9 25.7 + - - -
128A EDO 3.0 16.9 + - - -
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Residues in contact with HIS 118 (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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38A ILE* 3.3 38.1 - - + +
39A SER 3.5 15.7 + - - -
40A ASN* 5.2 2.4 + - - -
100A VAL 4.0 0.5 - - - +
101A PHE* 3.3 2.8 - - - -
102A THR* 2.8 53.1 + - - +
116A MSE 3.7 11.6 - - + +
117A ASP* 1.3 71.8 + - - +
119A SER* 1.3 63.4 + - - +
120A SER* 4.3 10.5 + - - -
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Residues in contact with SER 119 (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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38A ILE 2.9 7.1 + - - +
39A SER* 3.3 26.7 - - - -
40A ASN 3.7 0.5 + - - -
88A TRP* 4.4 12.0 - - - -
100A VAL 3.4 5.8 - - - -
101A PHE* 3.4 15.2 - - - +
117A ASP* 2.9 20.3 + - - -
118A HIS* 1.3 73.0 - - - +
120A SER* 1.3 61.6 + - - +
128A EDO 3.7 7.1 + - - -
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Residues in contact with SER 120 (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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40A ASN* 3.1 26.7 - - - -
88A TRP* 3.4 4.3 + - - -
99A GLY* 3.3 3.6 - - - -
100A VAL* 2.9 49.5 + - - +
118A HIS* 4.2 12.0 + - - -
119A SER* 1.3 76.8 - - - +
121A ASP* 1.3 65.4 + - - +
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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