Contacts of the strand formed by residues 116 - 124 (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 ALA 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B PHE* 5.2 0.7 - - + -
96B HIS 3.1 16.6 - - - +
97B TRP* 3.9 9.0 - - + -
104B GLY 4.2 3.6 - - - -
105B SER* 3.9 4.6 - - - -
114B TYR* 3.2 7.9 - - - +
115B ALA* 1.3 84.1 - - - +
117B GLU* 1.3 64.0 + - - +
147B PHE* 3.7 2.9 - - - -
148B LEU* 3.0 50.0 + - + +
223B VAL* 4.6 4.9 - - + -
226B PHE* 4.6 8.3 - - + -
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Residues in contact with GLU 117 (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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95B PHE* 3.1 8.0 - - - -
96B HIS* 2.8 44.7 + - + +
105B SER* 3.6 14.3 - - - -
106B GLU* 2.8 23.7 + - - +
107B HIS* 2.8 33.1 + - - -
116B ALA* 1.3 76.6 - - - +
118B LEU* 1.3 63.2 + - - +
119B HIS* 2.6 34.8 + - + +
145B GLY* 4.6 5.4 - - - -
146B ILE 3.4 16.6 - - - +
147B PHE* 3.7 12.1 - - + -
148B LEU* 4.3 0.4 - - - -
211B VAL* 5.2 0.9 - - - +
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Residues in contact with LEU 118 (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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93B PHE* 3.7 26.2 - - + -
94B HIS 3.4 17.5 - - - +
95B PHE* 3.6 33.0 - - + -
117B GLU* 1.3 72.5 - - - +
119B HIS* 1.3 68.2 + - - +
120B LEU* 4.0 19.3 - - + -
144B LEU 3.5 1.0 - - - +
145B GLY* 3.2 2.3 - - - -
146B ILE* 2.8 52.1 + - + +
148B LEU* 4.0 4.6 - - + +
184B LEU* 3.7 36.8 - - + +
216B ILE* 5.1 3.8 - - + -
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Residues in contact with HIS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PHE* 3.1 6.2 - - - +
94B HIS* 2.9 51.1 + - + +
96B HIS* 3.1 8.5 + + - -
106B GLU* 3.1 22.7 - - + -
107B HIS* 5.1 0.4 - - - -
117B GLU* 2.6 32.4 + - + -
118B LEU* 1.3 84.2 - - - +
120B LEU* 1.3 63.0 + - - +
121B VAL* 3.9 1.0 + - - -
143B VAL* 3.7 13.2 - - + -
144B LEU 3.5 2.0 - - - -
145B GLY* 3.9 4.0 - - - -
199B THR* 4.4 0.2 - - - -
209B TRP* 3.5 31.1 - + - -
301B ZN 2.1 33.3 - - - -
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Residues in contact with LEU 120 (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* 3.6 24.9 - - + +
90B LEU* 4.2 8.3 - - + -
92B GLN 3.8 3.1 - - - -
93B PHE* 3.9 27.1 - - + -
118B LEU* 4.0 14.8 - - + -
119B HIS* 1.3 73.4 - - - +
121B VAL* 1.3 61.0 + - - +
122B HIS* 3.0 24.5 + - + -
143B VAL* 3.3 1.8 - - - -
144B LEU* 2.9 55.8 + - + +
146B ILE* 3.9 28.5 - - + -
181B PRO* 4.2 11.9 - - + +
184B LEU* 5.4 1.6 - - + -
185B LEU* 4.6 5.2 - - + -
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Residues in contact with VAL 121 (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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90B LEU* 3.5 5.6 - - - +
91B ILE* 3.0 38.5 + - + -
92B GLN* 2.9 32.4 + - + +
94B HIS* 3.6 31.0 - - + +
119B HIS 4.2 0.9 - - - +
120B LEU* 1.3 72.5 - - - +
122B HIS* 1.3 66.2 + - - +
131B PHE* 4.1 18.8 - - + -
141B LEU* 4.4 8.5 - - + -
142B ALA 4.0 2.0 - - - -
143B VAL* 4.3 21.5 - - + -
198B LEU* 5.7 3.4 - - + -
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Residues in contact with HIS 122 (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* 2.7 32.2 + + - -
79B LEU* 3.6 38.0 - - + +
88B TYR* 3.6 18.4 - - + -
89B ARG 3.0 10.3 - - - +
90B LEU* 3.6 27.8 - - + +
91B ILE 4.6 0.2 - - - +
120B LEU* 3.0 32.6 + - + -
121B VAL* 1.3 73.1 - - - +
123B TRP* 1.3 61.2 + - - +
141B LEU* 3.2 10.2 - - - +
142B ALA* 2.8 40.1 + - + +
144B LEU* 4.2 5.2 - - + -
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Residues in contact with TRP 123 (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* 2.8 49.8 + - - +
88B TYR* 3.1 5.0 - - - -
89B ARG* 2.8 62.8 + - + +
91B ILE* 3.8 19.9 - - + +
122B HIS* 1.3 74.2 - - - +
124B ASN* 1.3 80.6 - - - +
125B THR* 3.3 20.5 + - + -
129B GLY* 3.1 36.1 - - - -
130B ASP* 3.7 15.0 - - + -
131B PHE* 3.8 20.4 - - + +
134B ALA* 3.9 8.1 - - + -
140B GLY 3.4 4.5 - - - +
141B LEU* 3.6 17.5 - - + -
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Residues in contact with ASN 124 (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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85B ASP* 4.3 9.3 + - - +
86B GLY* 5.3 1.0 - - - -
87B THR 3.6 11.6 + - - +
88B TYR* 3.3 25.0 + - + -
123B TRP* 1.3 78.9 - - - +
125B THR* 1.3 69.2 + - - +
127B LYS* 3.0 35.3 + - - +
128B TYR* 3.0 22.4 + - + +
134B ALA* 4.5 0.2 - - - +
139B ASP* 3.0 34.3 + - - +
140B GLY 2.7 18.9 + - - +
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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