Contacts of the strand formed by residues 94 - 104 (chain B) in PDB entry 2HZA
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 ASP 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B VAL* 4.4 4.0 - - + -
60B TYR 3.5 2.2 - - - +
61B GLU* 4.0 8.0 - - - +
89B HIS* 3.9 1.0 - - - +
90B ILE* 3.1 37.9 + - + +
91B ASN* 2.4 54.5 + - - +
93B ASP* 1.3 78.3 - - - +
95B CYS* 1.3 64.1 + - - +
122B ARG* 3.0 38.6 + - - -
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Residues in contact with CYS 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B TYR 3.9 0.5 - - - +
59B VAL* 3.2 8.1 - - - +
60B TYR* 2.8 46.5 + - + +
62B HIS* 3.7 31.6 - - - -
87B HIS* 3.0 23.1 - - + +
88B VAL 3.7 4.3 - - - -
90B ILE* 4.7 1.1 - - - -
94B ASP* 1.3 76.1 - - - +
96B LEU* 1.3 59.2 - - - +
301B NI 2.1 39.7 - - - -
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 4.5 13.7 - - + -
54A ALA 5.0 0.2 - - - +
55A VAL* 4.1 22.7 - - + -
100A VAL* 4.0 28.7 - - + -
129A LEU* 3.8 28.7 - - + -
57B SER* 5.0 1.3 - - - -
58B TYR 3.6 15.3 - - - +
59B VAL* 4.1 7.9 - - + -
86B LEU 3.8 0.5 - - - +
87B HIS* 3.4 2.8 - - - -
88B VAL* 2.8 44.4 + - + +
90B ILE* 4.0 13.7 - - + +
95B CYS* 1.3 74.5 - - - +
97B GLU* 1.3 69.5 + - - +
98B ILE* 4.7 6.0 - - + +
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU 3.5 1.2 - - - +
57B SER* 3.2 4.0 - - - -
58B TYR* 2.7 73.3 + - + +
60B TYR* 3.2 25.0 + - + -
71B ILE* 4.2 3.3 - - - +
72B VAL* 5.7 5.7 - - - +
75B GLN* 3.7 11.0 + - - -
85B THR* 3.8 13.9 - - + +
86B LEU 3.2 4.5 - - - +
87B HIS* 2.4 42.2 + - + +
96B LEU* 1.3 73.3 - - - +
98B ILE* 1.3 66.3 + - - +
99B ALA 4.1 0.2 - - - -
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A VAL* 3.7 17.7 - - + -
86A LEU* 4.6 2.4 - - + +
98A ILE* 3.6 46.7 - - + -
100A VAL* 3.4 33.2 - - + -
55B VAL* 3.7 16.6 - - + -
56B LEU 3.1 4.9 - - - +
57B SER* 4.1 12.8 - - - -
84B ALA 3.9 0.9 - - - +
85B THR* 3.3 4.1 - - - -
86B LEU* 2.8 46.9 + - + +
88B VAL* 6.2 0.4 - - + -
96B LEU* 4.7 6.7 - - + -
97B GLU* 1.3 80.4 - - - +
99B ALA* 1.3 61.1 + - - +
100B VAL 4.0 0.3 + - - -
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B VAL* 3.6 3.3 - - - -
56B LEU* 2.7 48.6 + - + +
58B TYR* 4.4 11.4 - - - +
75B GLN* 4.1 11.4 - - - +
82B SER* 5.6 0.4 - - - +
84B ALA 3.7 4.7 - - - +
85B THR* 3.7 15.5 - - - +
97B GLU 4.1 0.8 - - - -
98B ILE* 1.3 73.2 - - - +
100B VAL* 1.3 62.9 + - - +
101B LEU* 3.7 18.5 + - + +
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 3.8 19.1 - - + -
88A VAL* 4.0 17.5 - - + -
96A LEU* 3.9 23.3 - - + -
98A ILE* 3.2 33.9 - - + -
53B PHE* 4.5 4.7 - - + -
54B ALA 3.5 7.0 - - - +
55B VAL* 4.8 0.2 - - - +
82B SER* 4.1 0.9 + - - -
83B VAL* 3.0 44.2 + - + +
84B ALA* 2.9 15.0 + - + +
98B ILE 5.1 0.2 - - - +
99B ALA* 1.3 71.4 - - - +
101B LEU* 1.3 67.7 + - - +
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PHE* 3.3 9.9 - - - -
54B ALA* 2.9 32.7 + - + +
56B LEU* 4.2 26.2 - - + -
75B GLN* 5.5 0.4 - - - +
81B LEU 3.3 9.0 - - - +
82B SER* 4.3 7.0 - - - -
83B VAL* 4.0 1.1 - - - -
99B ALA* 4.0 21.3 - - + +
100B VAL* 1.3 81.3 - - - +
102B LYS* 1.3 62.7 + - - +
108B VAL* 3.7 36.6 - - + +
111B PHE* 3.6 38.4 - - + -
112B ALA* 5.1 1.6 - - + -
126B LEU* 4.4 7.9 - - + -
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ILE 5.1 4.8 + - - -
52B GLY* 3.5 11.4 - - - +
53B PHE* 3.3 38.3 - - + +
80B ASP 4.3 2.4 - - - +
81B LEU* 2.7 37.7 + - - +
83B VAL* 3.7 16.8 - - + +
101B LEU* 1.3 78.2 - - - +
103B GLY* 1.3 63.5 + - - +
108B VAL* 4.2 5.8 - - - -
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Residues in contact with GLY 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLN* 3.4 13.1 - - - -
52B GLY 3.0 32.8 + - - +
81B LEU* 4.3 6.1 - - - -
102B LYS* 1.3 81.6 - - - +
104B ASP* 1.3 65.3 + - - -
105B MSE 3.4 1.2 + - - -
108B VAL* 4.3 2.0 - - - +
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Residues in contact with ASP 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B THR* 3.1 31.5 - - - +
51B GLN* 3.5 13.5 + - - +
81B LEU* 4.6 4.2 - - + +
103B GLY* 1.3 69.6 - - - -
105B MSE 1.3 59.1 + - - +
106B GLY* 3.2 9.4 + - - -
107B ASP* 2.9 46.7 + - - +
108B VAL* 2.9 28.5 + - - +
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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