Contacts of the strand formed by residues 114 - 124 (chain H) in PDB entry 3BXB
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 CYS 114 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10H HIS* 3.3 41.3 - - - +
11H MET* 3.7 8.3 - - - -
12H LYS* 3.8 25.6 - - - +
110H LEU* 3.3 8.9 - - - +
111H GLN 3.0 34.7 + - - +
112H ASP 3.1 4.6 - - - +
113H GLY* 1.3 78.6 - - - +
115H LEU* 1.3 82.3 + - - +
116H ILE* 4.0 5.5 - - + +
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Residues in contact with LEU 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H ILE* 5.0 1.3 - - + -
9H MET* 4.2 18.6 - - + -
10H HIS 2.9 8.4 + - - +
11H MET* 3.2 14.5 - - + +
12H LYS 2.6 33.6 + - - +
68H THR* 4.2 13.2 - - + +
69H PHE* 3.4 37.5 - - + -
84H PHE* 3.5 38.1 - - + -
108H THR* 4.2 8.1 - - + -
109H SER 3.7 7.4 - - - +
110H LEU* 4.2 8.3 - - + -
114H CYS* 1.3 76.7 - - - +
116H ILE* 1.3 58.1 + - - +
117H TYR* 3.8 12.1 - - + +
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Residues in contact with ILE 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H LYS* 3.4 27.1 - - + +
14H TYR* 4.7 16.6 - - + -
107H ASP 3.5 6.4 - - - +
108H THR 3.9 0.2 - - - -
109H SER* 3.0 36.7 + - - +
111H GLN* 3.7 49.6 - - + +
114H CYS* 4.0 15.7 - - + +
115H LEU* 1.3 82.5 - - - +
117H TYR* 1.3 65.8 + - - +
118H ASN* 4.0 16.2 + - - +
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Residues in contact with TYR 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H MET* 4.0 15.0 - - + +
12H LYS 2.7 13.5 + - - +
13H LEU* 3.1 27.6 - - + -
14H TYR* 2.7 34.7 + - - -
41H MET* 4.8 4.5 - - - -
62H PHE 3.8 15.3 - - - -
63H NRQ 5.0 0.2 - - - -
66H SER* 2.6 46.3 + - - -
67H LYS 5.7 0.4 - - - -
68H THR* 4.6 3.0 + - - -
69H PHE* 3.4 15.6 - - - -
106H GLN* 3.6 22.2 - - - +
107H ASP 3.5 3.8 - - - -
108H THR* 3.4 25.6 - - + -
115H LEU* 3.8 21.3 - - + +
116H ILE* 1.3 79.6 - - - +
118H ASN* 1.3 57.8 + - - +
119H VAL* 4.1 1.3 - - + -
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Residues in contact with ASN 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H TYR* 3.2 18.8 - - + +
105H THR 3.9 0.7 - - - +
106H GLN* 3.5 2.5 - - - -
107H ASP* 3.1 56.1 + - - +
109H SER* 5.5 0.8 + - - -
116H ILE* 4.0 17.4 + - - +
117H TYR* 1.3 77.4 - - - +
119H VAL* 1.3 61.9 + - - +
120H LYS* 4.1 4.6 + - + +
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Residues in contact with VAL 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H LEU* 3.7 22.9 - - + -
14H TYR 2.7 13.5 + - - +
15H MET* 3.3 13.6 - - + +
16H GLU* 3.1 25.3 + - - +
61H SER* 3.6 33.2 - - - +
90H TRP* 4.5 5.4 - - + -
104H ALA* 4.7 1.1 - - + -
105H THR 3.4 13.5 - - - +
106H GLN* 3.9 14.4 - - + +
117H TYR* 4.7 0.9 - - + -
118H ASN* 1.3 75.6 - - - +
120H LYS* 1.3 68.3 + - - +
121H ILE* 3.8 19.7 - - + -
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Residues in contact with LYS 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLU* 4.5 12.7 + - - +
18E THR* 4.4 8.4 + - - -
23E HIS* 4.5 11.3 - - - +
122E ARG* 3.7 41.4 - - - +
16H GLU* 3.6 17.7 - - + +
104H ALA* 3.3 3.3 - - - -
105H THR* 2.8 51.5 + - - +
118H ASN* 5.2 4.3 - - + +
119H VAL* 1.3 79.6 - - - +
121H ILE* 1.3 61.6 + - - +
122H ARG* 6.2 0.7 - - - +
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Residues in contact with ILE 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E ARG* 5.1 1.5 - - - +
15H MET* 3.5 35.0 - - + -
16H GLU 2.9 10.8 + - - +
17H GLY* 3.1 22.7 - - - -
18H THR 3.2 3.0 + - - -
19H VAL* 5.0 2.5 - - + -
24H PHE* 4.5 9.0 - - + -
58H LEU* 3.6 25.1 - - + -
61H SER* 3.5 26.7 - - - +
102H LEU* 3.9 27.6 - - + -
103H THR 3.6 2.5 - - - -
104H ALA* 4.5 1.6 - - + -
119H VAL* 3.8 10.8 - - + -
120H LYS* 1.3 79.5 - - - +
122H ARG* 1.3 71.1 + - - +
123H GLY 4.7 1.1 - - - +
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Residues in contact with ARG 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E THR* 3.7 20.5 + - - +
105E THR* 3.5 37.6 + - + +
120E LYS* 3.9 39.7 + - - +
121E ILE 5.1 0.4 - - - -
122E ARG* 4.3 32.3 - - + +
17H GLY* 4.8 5.1 - - - -
18H THR* 3.2 36.5 + - - +
101H VAL 4.0 0.9 - - - +
102H LEU* 3.7 1.0 - - - -
103H THR* 2.8 48.0 + - - +
120H LYS* 6.2 1.0 - - - +
121H ILE* 1.3 82.1 + - - +
123H GLY* 1.3 58.5 + - - +
124H VAL* 4.3 5.9 + - + +
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Residues in contact with GLY 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E GLU* 4.0 2.3 - - - +
18H THR 2.8 14.5 + - - +
19H VAL* 3.4 5.2 - - - +
20H ASN 3.0 23.8 + - - -
101H VAL 3.1 9.9 - - - -
102H LEU* 4.0 12.0 - - - +
121H ILE 4.3 0.2 - - - -
122H ARG* 1.3 72.0 - - - +
124H VAL* 1.3 66.1 + - - +
126H PHE* 3.8 16.2 - - - -
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Residues in contact with VAL 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E GLU* 4.3 19.3 - - + -
92E ARG* 4.0 10.1 - - - +
93E VAL* 3.9 34.1 - - + -
103E THR* 4.3 20.4 - - + -
105E THR* 4.2 24.5 - - + -
175E LYS 5.7 0.2 - - - +
20H ASN* 3.4 6.7 - - - -
101H VAL* 2.8 37.2 + - + +
122H ARG* 4.4 3.6 - - + +
123H GLY* 1.3 80.7 - - - +
125H ASN* 1.3 61.4 + - + +
126H PHE* 3.1 12.7 + - - -
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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