Contacts of the strand formed by residues 111 - 116 (chain B) in PDB entry 3VI4
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 PHE 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B LYS* 4.9 6.7 - - + -
96B PRO* 4.8 5.4 - - + -
99B LEU* 3.4 42.4 - - + -
101B LEU* 4.9 3.8 - - + -
109B GLN 4.6 4.7 - - - -
110B THR* 1.3 78.4 - - - +
112B THR* 1.3 83.2 + - - +
113B LEU* 3.7 27.4 - - + -
406B PHE 3.6 0.3 - - - +
407B GLU* 3.3 3.7 - - - +
408B ILE* 2.6 87.7 + - + -
410B ILE* 4.9 4.7 - - + -
425B ILE* 4.8 1.8 - - + -
434B VAL* 4.9 3.6 - - + -
436B VAL* 4.5 24.7 - - + -
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Residues in contact with THR 112 (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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96B PRO* 3.7 12.5 - - - +
111B PHE* 1.3 88.0 - - - +
113B LEU* 1.3 64.4 + - - +
114B LYS* 4.4 19.1 + - - -
405B GLN* 5.4 10.8 - - + +
406B PHE 3.1 5.4 - - - +
407B GLU* 3.6 28.5 - - + +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE* 3.8 30.7 - - + -
95B GLN 4.0 1.3 - - - +
96B PRO* 4.0 9.9 - - + -
111B PHE* 3.7 23.6 - - + -
112B THR* 1.3 75.2 - - - +
114B LYS* 1.3 64.2 + - - +
115B PHE 4.2 0.2 - - - -
364B LEU* 3.8 28.3 - - + -
405B GLN* 3.2 5.9 - - - +
406B PHE* 2.5 50.0 + - + +
408B ILE* 4.0 13.5 - - + -
425B ILE* 4.9 5.4 - - + +
434B VAL* 3.5 31.0 - - + -
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Residues in contact with LYS 114 (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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75B VAL* 3.9 14.0 - - + +
93B GLN 3.3 4.5 - - - +
94B ILE* 3.5 2.6 - - - +
95B GLN* 3.0 51.4 + - + +
112B THR* 4.5 16.8 + - - -
113B LEU* 1.3 76.2 - - - +
115B PHE* 1.3 61.4 + - - +
403B GLU* 4.9 16.4 - - + +
404B VAL 3.4 9.6 - - - +
405B GLN* 3.3 35.8 - - + +
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Residues in contact with PHE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B GLN* 3.2 44.6 - - + -
94B ILE* 3.7 22.9 - - + +
113B LEU* 4.2 0.8 + - + -
114B LYS* 1.3 74.1 - - - +
116B LYS* 1.3 63.2 + - - +
117B ARG* 3.9 24.2 - - + -
359B SER 6.1 0.4 - - - -
362B VAL* 3.4 35.4 - - + -
398B ILE* 4.4 11.2 - - + -
402B ASP 3.7 0.2 - - - +
403B GLU* 3.2 4.2 - - - +
404B VAL* 2.7 59.0 + - + +
406B PHE* 4.3 13.4 - - + -
427B PRO* 4.7 0.7 - - + -
430B PHE* 3.9 17.9 - + - -
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Residues in contact with LYS 116 (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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75B VAL* 4.1 21.3 - - + -
76B THR 3.4 26.3 + - - +
77B ASN* 4.6 12.7 - - - +
78B ARG* 5.4 9.4 - - - +
92B HIS 5.1 0.9 - - - +
93B GLN* 2.9 33.9 + - - +
115B PHE* 1.3 79.4 - - - +
117B ARG* 1.3 68.7 + - - +
118B ALA* 3.4 2.4 + - - -
401B GLY* 3.4 27.7 + - - +
402B ASP 3.3 7.4 - - - +
403B GLU* 2.8 39.2 + - + +
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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