Contacts of the strand formed by residues 99 - 104 (chain B) in PDB entry 1V1A
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 GLY 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B GLU* 3.6 11.9 - - - -
93B TYR* 4.8 3.4 - - - -
94B LEU* 5.2 0.9 - - - -
97B GLY 3.3 5.4 + - - -
98B GLN* 1.3 92.8 + - - +
100B ARG* 1.3 60.7 + - - +
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Residues in contact with ARG 100 (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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58A GLU 3.3 25.5 + - - -
59A ASP* 4.2 7.9 - - - +
60A GLU* 4.7 6.1 + - - +
81A ARG* 5.6 1.4 - - - +
91B ARG* 4.7 0.3 - - - +
92B GLU* 3.4 42.1 + - - +
98B GLN* 5.5 2.0 - - + +
99B GLY* 1.3 74.2 - - - +
101B VAL* 1.3 72.4 + - - +
102B PHE* 3.5 42.9 - - + -
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 3.3 39.0 - - + -
90B LEU 3.5 2.7 - - - +
91B ARG* 4.4 15.0 - - + -
100B ARG* 1.3 86.0 + - - +
102B PHE* 1.3 71.8 + - - +
103B TYR* 3.9 29.7 + - + +
169B THR* 4.7 10.0 + - - +
247B VAL* 6.1 2.9 - - + -
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Residues in contact with PHE 102 (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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59A ASP* 3.7 28.3 - - + +
60A GLU* 3.6 25.8 - - + -
61A LEU* 6.5 0.7 - - + -
22B LEU* 3.6 26.0 - - + -
89B TYR* 3.1 5.5 - - - +
90B LEU* 2.8 50.1 + - + +
92B GLU* 4.3 8.7 - - + -
100B ARG* 3.5 57.0 - - - -
101B VAL* 1.3 77.1 - - - +
103B TYR* 1.3 61.3 + - - +
104B TYR* 3.9 17.9 - - + +
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Residues in contact with TYR 103 (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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85A PHE* 5.2 8.7 - - - +
11B LEU* 4.4 2.7 - - + -
88B LEU 5.0 0.2 - - - -
89B TYR* 3.6 20.2 - + + -
101B VAL* 3.9 26.2 + - + +
102B PHE* 1.3 70.7 - - - +
104B TYR* 1.3 76.1 + - - +
105B ARG* 3.5 28.7 + - + -
167B ARG* 3.7 16.6 - - + +
169B THR* 3.6 35.8 - - + +
170B LEU* 3.6 22.4 - - + -
1302B KDG 2.8 43.2 + - - -
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Residues in contact with TYR 104 (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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59A ASP* 4.2 6.6 + - - -
61A LEU* 3.9 13.7 - - + +
85A PHE* 3.5 30.9 - + + +
86A THR 2.7 32.9 + - - -
88A LEU* 3.7 12.8 - - + -
104A TYR* 3.7 40.7 - - + -
85B PHE* 3.9 3.6 - - - -
87B GLY* 3.6 4.3 - - - -
88B LEU* 2.9 44.7 + - + +
90B LEU* 3.5 33.7 - - + -
102B PHE* 3.9 15.0 - - + +
103B TYR* 1.3 85.5 - - - +
105B ARG* 1.3 56.9 + - - +
106B LYS 3.9 0.7 - - - +
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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