Contacts of the strand formed by residues 101 - 111 (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 VAL 101 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E VAL* 4.1 37.2 - - + -
101E VAL* 4.6 1.1 - - + -
103E THR* 4.5 3.0 - - + +
175E LYS* 6.0 2.7 - - - -
93H VAL* 3.8 28.0 - - + -
94H THR 3.5 5.6 - - - +
95H THR* 4.7 11.9 - - + +
99H GLY 4.0 8.3 - - - +
100H GLY* 1.3 77.2 - - - +
102H LEU* 1.3 65.0 + - - +
103H THR* 4.2 9.9 - - + -
122H ARG 4.0 0.7 - - - +
123H GLY* 3.1 2.1 - - - -
124H VAL* 2.8 43.3 + - + +
125H ASN* 5.0 0.7 - - + +
126H PHE* 3.5 3.4 - - - -
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Residues in contact with LEU 102 (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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19H VAL* 4.4 4.5 - - + -
57H ILE* 3.7 51.4 - - + +
58H LEU* 4.4 1.3 - - + -
60H THR* 6.0 1.3 - - - +
61H SER* 4.6 7.0 - - - +
92H ARG* 4.1 1.2 - - - +
93H VAL* 3.7 0.7 - - - -
94H THR* 2.9 47.6 + - - +
96H TYR* 4.8 4.3 - - + -
101H VAL* 1.3 75.4 - - - +
103H THR* 1.3 66.4 + - - +
104H ALA* 4.5 9.8 - - + +
121H ILE* 3.9 31.0 - - + -
122H ARG 3.7 2.0 - - - -
123H GLY* 4.2 9.6 - - - -
126H PHE* 4.1 10.3 - - + -
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Residues in contact with THR 103 (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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101E VAL* 4.4 4.9 - - + -
103E THR* 3.1 35.4 + - + -
122E ARG* 4.0 12.4 - - - +
124E VAL* 4.1 19.3 - - + -
92H ARG 3.4 6.7 - - - +
93H VAL* 4.0 25.6 - - + -
101H VAL* 4.2 1.5 - - + -
102H LEU* 1.3 75.6 - - - +
104H ALA* 1.3 61.3 + - - +
121H ILE* 3.6 2.9 - - - +
122H ARG* 2.8 47.7 + - - +
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Residues in contact with ALA 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E ARG* 5.1 1.1 - - - +
124E VAL* 5.0 0.6 - - - +
61H SER* 3.9 17.7 - - - +
90H TRP* 3.5 21.1 - - + -
91H GLU* 3.4 3.6 - - - -
92H ARG* 3.0 36.2 + - + +
102H LEU* 4.5 9.4 - - + +
103H THR* 1.3 77.7 - - - +
105H THR* 1.3 64.8 + - - +
119H VAL* 4.7 0.9 - - + -
120H LYS 3.3 9.9 - - - +
121H ILE* 4.5 6.3 - - + -
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Residues in contact with THR 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E THR* 4.0 18.6 - - + -
21E ASN* 5.7 2.2 - - + +
122E ARG* 3.1 41.3 + - + -
124E VAL* 4.3 5.4 - - + -
90H TRP 3.6 4.0 - - - -
91H GLU* 4.1 17.0 - - + +
104H ALA* 1.3 78.1 - - - +
106H GLN* 1.3 62.5 + - - +
118H ASN 3.9 0.7 - - - +
119H VAL* 3.4 4.1 - - - +
120H LYS* 2.8 48.1 + - - +
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Residues in contact with GLN 106 (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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61H SER 4.7 0.8 + - - +
63H NRQ 3.0 23.0 + - - -
88H PHE 4.4 1.2 - - - +
89H THR* 3.3 10.1 - - - +
90H TRP* 2.9 67.7 + - + +
105H THR* 1.3 76.2 - - - +
107H ASP* 1.3 82.5 + - - +
108H THR* 2.4 30.3 + - - -
117H TYR* 3.6 23.2 - - - +
118H ASN 3.5 4.3 - - - +
119H VAL* 3.9 21.3 - - + +
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Residues in contact with ASP 107 (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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89H THR* 3.4 10.5 - - + +
106H GLN* 1.3 82.9 - - - +
108H THR* 1.3 62.1 + - - +
109H SER* 4.5 6.6 + - - -
116H ILE 3.5 4.9 - - - +
118H ASN* 3.1 53.6 + - - +
181H LYS* 2.7 36.3 + - - -
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Residues in contact with THR 108 (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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63H NRQ 4.8 0.2 + - - -
68H THR* 4.6 0.7 - - - +
84H PHE* 4.2 22.2 - - + -
87H GLY* 3.3 0.7 - - - -
88H PHE* 2.7 54.0 + - + -
106H GLN* 2.4 33.4 + - - -
107H ASP* 1.3 72.0 - - - +
109H SER* 1.3 61.8 + - - +
115H LEU* 4.2 5.2 - - + -
116H ILE 3.5 2.2 - - - -
117H TYR* 3.4 26.9 - - + -
181H LYS* 2.8 25.6 + - - -
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Residues in contact with SER 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H PHE* 4.0 4.9 - - - -
86H GLU 4.4 7.0 - - - -
87H GLY* 4.2 8.1 - - - -
107H ASP* 4.5 6.6 + - - -
108H THR* 1.3 76.8 - - - +
110H LEU* 1.3 61.8 + - - +
111H GLN* 3.6 24.4 + - - -
115H LEU* 3.7 6.2 - - - +
116H ILE* 3.0 37.3 + - - +
118H ASN* 5.5 0.3 + - - -
181H LYS* 4.4 8.3 - - - -
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Residues in contact with LEU 110 (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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4H LEU* 3.8 40.4 - - + +
5H ILE* 4.3 5.4 - - + -
9H MET* 3.9 15.0 - - + -
84H PHE* 3.5 31.6 - - + -
85H PRO* 4.3 13.0 + - + +
109H SER* 1.3 73.4 - - - +
111H GLN* 1.3 62.6 + - - +
112H ASP 4.0 2.4 + - - +
113H GLY* 3.9 13.5 - - - +
114H CYS 3.3 33.0 - - - +
115H LEU* 4.2 7.4 - - + -
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Residues in contact with GLN 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H SER* 3.6 20.6 + - - +
110H LEU* 1.3 74.8 - - - +
112H ASP* 1.3 73.2 + - - +
113H GLY 3.6 0.4 - - - -
114H CYS* 3.0 23.3 + - - +
116H ILE* 3.7 33.7 - - + +
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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