Contacts of the strand formed by residues 88 - 97 (chain B) in PDB entry 3V3H
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 TYR 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B VAL* 3.2 6.3 - - - -
79B LEU* 2.8 41.2 + - + +
84B LEU* 3.7 37.0 - - + +
85B ASP* 3.5 23.6 + - - +
86B GLY 4.4 0.2 - - - -
87B THR* 1.3 80.1 - - - +
89B ARG* 1.3 62.4 + - - +
122B HIS* 3.6 15.7 - - + -
123B TRP 3.1 5.2 - - - -
124B ASN* 3.3 39.7 + - + -
139B ASP* 3.0 26.5 + - - +
141B LEU 3.5 21.3 + - - -
142B ALA* 3.5 22.7 - - + -
208B THR* 4.8 2.4 + - - -
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Residues in contact with ARG 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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72B ASP* 3.0 30.2 + - + +
73B SER* 4.4 6.6 + - - +
74B GLN 3.7 16.2 - - - -
75B ASP* 3.4 36.9 + - - +
77B ALA 3.7 5.6 - - - -
78B VAL* 4.4 4.6 - - + +
88B TYR* 1.3 73.1 - - - +
90B LEU* 1.3 63.1 + - - +
91B ILE 3.4 1.2 + - - -
122B HIS* 3.0 5.2 - - - -
123B TRP* 2.8 67.2 + - + +
125B THR* 3.4 31.6 - - + +
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Residues in contact with LEU 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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51B TYR* 4.1 18.6 - - + -
54B ALA* 4.2 10.1 - - + -
70B PHE* 3.8 49.9 - - + +
71B ASP 4.8 0.5 - - - +
72B ASP* 3.4 20.0 - - - +
77B ALA* 3.3 20.2 + - + +
89B ARG* 1.3 71.1 - - - +
91B ILE* 1.3 59.5 + - - +
92B GLN 3.8 15.5 - - - +
120B LEU* 4.2 13.5 - - + -
121B VAL 3.5 16.8 - - - +
122B HIS* 3.6 31.5 - - + +
181B PRO* 4.2 5.8 - - + -
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Residues in contact with ILE 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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69B GLU* 3.7 2.6 - - + +
70B PHE* 2.9 30.6 + - - +
72B ASP* 3.4 24.5 - - - +
89B ARG 3.4 0.4 + - - -
90B LEU* 1.3 75.3 - - - +
92B GLN* 1.3 73.3 + - + +
121B VAL* 3.0 29.1 + - + +
122B HIS 4.6 0.2 - - - +
123B TRP* 3.8 18.8 - - + -
131B PHE* 3.8 41.7 - - + -
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Residues in contact with GLN 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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67B ASN* 3.5 29.3 + - + +
68B VAL 3.1 17.0 - - - +
69B GLU* 4.3 4.7 - - + -
70B PHE* 4.1 2.9 - - - -
90B LEU* 3.8 7.3 - - - +
91B ILE* 1.3 96.2 - - + +
93B PHE* 1.3 65.7 + - - +
94B HIS* 2.8 34.4 + - - -
121B VAL* 2.9 45.3 + - + +
131B PHE* 5.8 4.6 - - + -
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Residues in contact with PHE 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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66B PHE* 3.9 0.8 - + - +
67B ASN* 3.4 2.3 - - - -
68B VAL* 2.9 66.2 + - + -
70B PHE* 3.5 31.0 - + - -
92B GLN* 1.3 78.5 - - - +
94B HIS* 1.3 65.5 + - - +
95B PHE* 3.8 22.2 - + - -
118B LEU* 3.7 20.6 - - + -
119B HIS 3.1 14.4 - - - +
120B LEU* 3.9 22.0 - - + -
160B VAL* 4.1 7.6 - - + -
179B PHE* 3.5 33.9 - + - -
181B PRO* 4.4 1.6 - - + -
184B LEU* 3.8 11.4 - - + -
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Residues in contact with HIS 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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64B HIS* 6.1 2.0 - - - -
65B ALA* 5.0 7.0 - - + -
66B PHE* 3.1 22.4 - - - +
67B ASN* 3.5 9.8 + - - +
92B GLN* 2.8 25.6 + - - -
93B PHE* 1.3 74.9 - - - +
95B PHE* 1.3 75.3 + - - +
96B HIS* 3.4 11.9 - + - -
118B LEU* 3.4 5.4 - - - +
119B HIS* 2.9 41.1 + - + -
121B VAL* 3.6 18.4 - - + -
301B ZN 2.1 37.9 - - - -
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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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65B ALA* 4.0 6.8 - - - +
66B PHE* 3.5 32.5 + + - -
93B PHE* 3.8 26.5 - + - -
94B HIS* 1.3 81.5 - - - +
96B HIS* 1.3 73.0 + - - +
97B TRP* 3.5 29.0 - - + -
116B ALA* 5.2 0.4 - - + -
117B GLU 3.1 7.6 - - - +
118B LEU* 3.6 39.9 - - + -
148B LEU* 3.9 22.7 - - + -
157B LEU* 3.9 21.5 - - + -
160B VAL* 4.3 3.4 - - + -
184B LEU* 4.6 5.6 - - + -
216B ILE* 5.8 0.9 - - + -
226B PHE* 3.8 19.1 - + + -
244B ASN* 4.0 5.2 + - - -
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Residues in contact with HIS 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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7B PHE* 5.8 0.7 - + - -
64B HIS* 6.0 3.1 - + - -
94B HIS* 3.4 7.0 + + - -
95B PHE* 1.3 79.6 + - - +
97B TRP* 1.3 61.8 + - - +
104B GLY 3.3 12.9 - - - +
106B GLU* 3.3 31.2 + - + -
116B ALA* 3.1 6.6 - - - +
117B GLU* 2.8 38.7 + - + +
119B HIS* 3.1 17.4 + + - -
199B THR* 3.6 5.4 - - - -
200B THR* 4.9 13.5 - - + -
244B ASN* 2.8 29.9 + - - +
245B TRP* 4.2 0.7 - - + -
301B ZN 2.1 37.4 - - - -
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Residues in contact with TRP 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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65B ALA* 4.4 3.8 - - + -
66B PHE* 4.0 18.2 - + - -
95B PHE* 3.5 40.4 - - + -
96B HIS* 1.3 76.3 - - - +
98B GLY* 1.3 71.2 + - - +
104B GLY* 3.5 8.4 + - - -
115B ALA 3.7 13.7 - - - +
116B ALA* 3.9 7.6 - - + -
223B VAL* 4.8 4.7 - - + -
226B PHE* 3.4 46.7 + + + -
227B ARG* 4.0 8.1 - - + +
229B LEU* 3.8 12.6 - - + -
241B MET* 2.8 54.2 + - + -
242B VAL* 4.0 1.5 - - - +
243B ASP* 3.0 22.0 + - - -
244B ASN* 3.0 29.3 + - - +
245B TRP* 3.5 2.6 - - - -
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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