Contacts of the strand formed by residues 51 - 61 (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 GLN 51 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B THR* 1.3 112.0 + - + +
52B GLY* 1.3 58.4 + - - +
103B GLY* 3.4 21.5 - - - -
104B ASP* 3.5 13.9 + - - +
105B MSE 4.2 2.7 - - - -
130B PRO* 3.5 6.6 - - - +
131B LYS* 2.9 30.4 + - + +
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Residues in contact with GLY 52 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B GLN* 1.3 76.1 - - - +
53B PHE* 1.3 69.1 + - - -
102B LYS* 3.5 7.6 - - - +
103B GLY* 3.0 34.4 + - - +
105B MSE 4.0 8.5 - - - +
108B VAL* 5.2 0.5 - - - +
129B LEU 3.7 9.2 - - - -
131B LYS* 3.9 8.7 - - - -
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Residues in contact with PHE 53 (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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88A VAL* 4.5 13.5 - - + -
89A HIS 5.4 0.2 - - - -
90A ILE* 3.4 57.9 - - + -
96A LEU* 4.6 13.2 - - + -
52B GLY* 1.3 78.3 - - - -
54B ALA* 1.3 64.9 + - - +
83B VAL* 4.5 8.3 - - + -
100B VAL* 4.5 10.3 - - + -
101B LEU 3.3 17.7 - - - -
102B LYS* 3.3 45.1 - - + -
105B MSE 3.7 7.0 - - - +
108B VAL* 5.7 0.7 - - - -
129B LEU* 2.8 44.3 + - + +
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Residues in contact with ALA 54 (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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96A LEU* 5.5 0.2 - - - -
53B PHE* 1.3 80.5 - - - +
55B VAL* 1.3 66.0 + - - +
100B VAL* 3.5 6.8 - - - +
101B LEU* 2.9 32.7 + - + +
105B MSE 5.4 0.7 - - - -
108B VAL* 3.6 30.5 - - + -
126B LEU* 4.1 11.0 - - + -
127B GLN 3.1 13.2 - - - +
128B CYS* 4.2 7.4 - - - +
129B LEU* 4.4 2.4 - - - +
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Residues in contact with VAL 55 (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* 5.3 4.5 - - + -
57A SER* 4.6 15.3 - - - +
96A LEU* 4.0 24.5 - - + -
98A ILE* 3.8 24.9 - - + -
54B ALA* 1.3 79.0 - - - +
56B LEU* 1.3 61.7 + - - +
57B SER* 4.1 3.7 + - - +
98B ILE* 3.7 26.0 - - + -
99B ALA 3.6 2.7 - - - -
100B VAL* 4.8 0.4 - - + -
125B HIS* 3.6 2.8 + - - +
126B LEU* 3.5 5.0 - - - +
127B GLN* 2.8 44.9 + - + +
129B LEU* 4.7 7.2 - - + -
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Residues in contact with LEU 56 (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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54B ALA 4.2 0.2 - - - -
55B VAL* 1.3 74.0 - - - +
57B SER* 1.3 60.2 + - - +
58B TYR* 3.6 27.0 - - + -
75B GLN* 6.4 0.2 - - - -
97B GLU 3.5 1.4 - - - +
98B ILE* 3.1 4.5 - - - -
99B ALA* 2.7 50.8 + - + +
101B LEU* 4.2 15.3 - - + -
111B PHE* 5.6 1.1 - - + -
112B ALA* 3.7 22.0 - - + -
115B VAL* 4.0 24.2 - - + -
116B ILE* 3.7 21.1 - - + -
125B HIS 3.4 10.5 - - - +
126B LEU* 3.7 24.5 - - + -
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Residues in contact with SER 57 (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* 4.5 12.8 - - - +
127A GLN* 2.7 28.4 + - - -
55B VAL* 4.1 3.4 + - - +
56B LEU* 1.3 76.0 - - - +
58B TYR* 1.3 66.4 + - - +
96B LEU* 5.0 2.5 - - - -
97B GLU 3.2 8.5 - - - -
98B ILE* 4.1 16.4 - - - -
116B ILE* 4.4 0.7 - - - +
123B HIS 3.5 1.5 - - - +
124B GLY* 3.3 0.5 - - - -
125B HIS* 2.8 41.3 + - - +
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Residues in contact with TYR 58 (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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56B LEU* 3.6 35.7 - - + -
57B SER* 1.3 80.8 - - - +
59B VAL* 1.3 63.4 + - - +
60B TYR* 3.6 23.1 - + - -
71B ILE* 4.2 5.6 - - + -
75B GLN* 3.2 19.6 + - - -
85B THR* 4.6 0.7 - - - +
95B CYS 3.9 0.3 - - - +
96B LEU* 3.6 6.0 - - - +
97B GLU* 2.7 70.0 + - + +
99B ALA* 4.4 7.8 - - + +
115B VAL* 3.7 14.4 - - + -
116B ILE* 3.5 28.9 - - + -
121B VAL* 3.8 13.0 - - + -
122B ARG 3.7 6.1 - - - +
123B HIS 3.9 4.3 - - - -
124B GLY* 3.9 1.3 - - - -
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Residues in contact with VAL 59 (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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129A LEU* 4.0 24.9 - - + -
58B TYR* 1.3 80.3 - - - +
60B TYR* 1.3 69.2 + - - +
90B ILE* 4.5 10.3 - - + -
94B ASP* 4.4 11.4 - - + -
95B CYS 3.2 10.5 - - - +
96B LEU* 4.1 9.0 - - + -
121B VAL* 3.4 2.6 - - - +
122B ARG* 2.7 67.1 + - + +
123B HIS* 3.9 22.4 - - + -
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Residues in contact with TYR 60 (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* 3.6 27.1 - + - -
59B VAL* 1.3 80.0 - - - +
61B GLU* 1.3 71.6 + - - +
62B HIS* 3.5 17.6 + - + -
67B LEU* 3.9 11.7 - - + -
68B ALA* 4.0 24.4 - - + +
71B ILE* 3.8 18.3 - - + +
72B VAL* 6.0 1.7 - - - +
87B HIS* 3.1 20.8 - - - -
94B ASP* 4.3 5.6 - - - -
95B CYS* 2.8 48.6 + - + -
97B GLU* 3.2 31.6 + - + -
120B GLY 3.2 16.6 - - - +
121B VAL* 4.3 4.7 - - + -
122B ARG* 4.4 2.5 - - - +
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Residues in contact with GLU 61 (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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60B TYR* 1.3 78.5 - - - +
62B HIS* 1.3 64.5 + - - +
63B GLU* 3.4 1.3 - - + +
64B LYS* 3.4 31.6 - - + +
67B LEU* 3.8 7.1 - - - +
93B ASP* 3.0 20.2 - - + +
94B ASP* 4.0 10.2 + - - +
120B GLY* 3.8 6.5 + - - +
122B ARG* 4.2 5.4 - - - +
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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