Contacts of the strand formed by residues 88 - 97 (chain B) in PDB entry 1DVQ
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 HIS 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A VAL* 3.7 25.9 - - + +
94A VAL 3.3 13.2 - - - +
118A THR* 4.1 8.6 + - - +
119A THR 5.5 0.2 - - - -
120A ALA* 5.0 1.8 + - - +
75B THR* 4.0 9.8 + - - +
76B LYS* 3.7 17.2 - - - +
86B PRO* 4.3 6.7 - - - +
87B PHE* 1.3 102.6 - + - +
89B GLU* 1.3 65.1 + - - +
90B HIS 3.2 15.9 - - - +
112B SER 5.1 1.0 + - - -
113B PRO 4.3 5.7 + - - -
114B TYR 3.7 29.8 - - - -
115B SER* 3.7 7.6 + - - -
116B TYR* 3.8 34.7 - + + -
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Residues in contact with GLU 89 (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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68A ILE* 4.1 21.2 - - + +
94A VAL* 2.8 36.3 + - + +
95A PHE* 4.0 8.5 - - - -
96A THR* 2.6 28.4 + - - +
74B ASP* 3.9 4.7 - - - +
76B LYS* 2.8 53.9 + - - +
87B PHE 3.9 1.4 + - - +
88B HIS* 1.3 74.7 - - - +
90B HIS* 1.3 75.7 + - + +
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Residues in contact with HIS 90 (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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35A LYS* 6.2 2.0 - - - -
41A TRP* 5.9 3.1 - + - -
92A GLU 5.6 0.2 - - - +
94A VAL* 4.0 24.4 + - + +
72B GLU* 3.2 27.8 + - + -
73B ILE 3.1 16.6 - - - +
74B ASP* 4.2 5.2 - - - +
75B THR* 3.3 14.1 - - - -
88B HIS* 3.2 14.1 - - - +
89B GLU* 1.3 94.2 + - + +
91B ALA* 1.3 58.7 + - - +
92B GLU* 2.6 43.9 + - + +
116B TYR* 4.4 3.6 + - - -
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Residues in contact with ALA 91 (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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71B VAL 3.7 0.7 - - - +
72B GLU* 3.5 3.3 - - - +
73B ILE* 2.9 47.2 + - + +
75B THR* 3.8 19.0 + - + -
90B HIS* 1.3 76.0 - - - +
92B GLU* 1.3 61.1 - - - +
93B VAL* 5.4 2.2 - - + -
109B ALA* 5.8 1.1 - - + -
111B LEU* 4.9 2.5 - - + -
116B TYR* 3.7 36.3 - - + -
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Residues in contact with GLU 92 (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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41A TRP* 5.7 1.2 - - - -
70A LYS* 4.8 2.8 + - - +
90A HIS 5.5 0.3 - - - +
92A GLU* 2.5 46.4 + - + +
94A VAL* 3.5 12.0 - - + +
116A TYR* 2.8 23.6 + - - -
70B LYS* 3.1 35.1 + - + +
71B VAL 3.4 2.9 - - - +
72B GLU* 3.9 10.1 - - + +
90B HIS* 2.6 40.7 + - + +
91B ALA* 1.3 73.8 - - - +
93B VAL* 1.3 65.9 + - - +
94B VAL* 4.1 1.7 + - + -
116B TYR* 3.7 8.9 + - - -
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Residues in contact with VAL 93 (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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87A PHE* 4.3 4.9 - - + -
88A HIS* 3.6 26.2 - - + +
116A TYR* 4.6 2.2 - - - -
69B TYR 3.6 1.2 - - - +
70B LYS* 3.3 2.1 - - - -
71B VAL* 2.7 48.9 + - + +
73B ILE* 5.1 10.3 - - + -
91B ALA* 5.4 2.2 - - + -
92B GLU* 1.3 81.6 - - - +
94B VAL* 1.3 62.3 + - - +
95B PHE* 4.1 16.8 - - + -
107B ILE* 4.1 21.3 - - + -
116B TYR* 6.0 0.7 - - + -
118B THR* 3.4 29.2 - - + +
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Residues in contact with VAL 94 (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 HIS* 3.3 10.6 - - - +
89A GLU* 2.8 43.5 + - + -
90A HIS* 3.8 22.1 + - + +
92A GLU* 3.4 27.4 - - + +
41B TRP* 3.9 13.5 - - + -
68B ILE* 3.9 12.6 - - + -
69B TYR 3.2 9.2 - - - +
70B LYS* 4.0 21.8 - - + -
92B GLU* 4.3 2.2 + - + +
93B VAL* 1.3 78.6 - - - +
95B PHE* 1.3 64.8 + - - +
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Residues in contact with PHE 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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87A PHE* 3.4 58.3 - + + +
89A GLU* 4.0 8.5 - - - -
12B LEU* 4.3 21.3 - - + -
64B PHE* 4.5 13.5 - + - -
68B ILE* 3.5 1.3 - - - -
69B TYR* 2.7 60.6 + + + -
71B VAL* 3.8 25.8 - - + -
93B VAL* 4.1 9.0 - - + -
94B VAL* 1.3 78.7 - - - +
96B THR* 1.3 68.6 + - - +
97B ALA* 3.9 6.0 + - + -
105B TYR* 4.1 16.6 - + - -
107B ILE* 4.3 8.1 - - + -
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Residues in contact with THR 96 (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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76A LYS* 4.1 5.3 + - - +
87A PHE* 4.1 8.3 + - - +
89A GLU* 2.7 30.9 + - - -
67B GLY* 3.4 14.6 - - - +
68B ILE* 3.7 12.6 - - + +
95B PHE* 1.3 80.9 - - - +
97B ALA* 1.3 72.6 + - - +
98B ASN* 3.2 9.4 + - + +
105B TYR* 4.5 4.2 + - - -
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Residues in contact with ALA 97 (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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64B PHE* 3.9 23.3 - - + +
65B VAL 4.2 7.6 - - - +
66B GLU* 3.6 18.9 - - - +
67B GLY 2.8 11.2 + - - +
69B TYR* 3.8 27.1 - - + -
95B PHE* 3.9 4.2 + - + -
96B THR* 1.3 74.5 - - - +
98B ASN* 1.3 63.3 + - - +
99B ASP* 5.3 1.3 - - + +
105B TYR* 3.6 15.0 - - + +
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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