Contacts of the strand formed by residues 88 - 94 (chain C) in PDB entry 1V8C
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 88 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C ALA 4.9 1.2 - - - +
86C GLY* 3.5 3.3 + - - -
87C GLY* 1.3 80.0 - - - +
89C PHE* 1.3 81.5 + - - -
146C GLU* 6.0 0.4 - - - -
147C VAL 3.0 12.8 - - - -
148C GLU* 4.1 6.7 - - - -
152C ALA* 4.3 0.7 - - - -
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Residues in contact with PHE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C TYR* 3.7 28.5 - + + -
7C ALA 5.4 0.7 - - - -
81C PHE* 3.6 24.0 - + - -
85C ALA* 3.4 42.4 - - + -
86C GLY 4.2 6.3 - - - -
88C GLY* 1.3 86.9 - - - -
90C GLU* 1.3 60.9 + - - +
145C VAL 4.0 0.2 - - - +
146C GLU* 3.3 5.9 - - - +
147C VAL* 2.9 31.0 + - - -
152C ALA* 3.9 13.5 - - + -
153C GLU* 3.5 38.8 - - + -
156C PHE* 3.8 27.4 - + + -
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Residues in contact with GLU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C TYR* 4.9 8.7 + - - -
89C PHE* 1.3 77.7 - - - +
91C ARG* 1.3 98.3 + - - +
92C THR* 3.3 13.3 + - - -
144C ARG* 3.4 46.5 + - + +
145C VAL 3.1 13.9 - - - +
146C GLU* 4.2 8.1 - - + +
156C PHE* 3.7 8.0 - - - -
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Residues in contact with ARG 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ASN* 3.3 13.8 - - - +
6C TYR* 3.0 21.2 + - - -
77C THR* 5.2 5.1 - - - +
79C ASP* 2.7 36.7 + - - -
90C GLU* 1.3 87.8 + - - +
92C THR* 1.3 71.0 + - - +
93C PHE* 3.7 29.4 - - + -
143C LEU 3.7 1.0 - - - +
145C VAL* 2.9 28.8 + - - +
156C PHE* 3.7 23.5 - - + -
160C ALA* 3.9 21.6 - - - +
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Residues in contact with THR 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLU* 3.3 12.2 + - - -
91C ARG* 1.3 85.4 - - - +
93C PHE* 1.3 64.3 + - - +
94C GLY 4.3 0.9 + - - -
130C VAL* 3.9 12.4 - - + +
142C GLN* 3.8 36.5 - - + +
143C LEU 3.3 9.9 - - - +
144C ARG* 3.9 11.6 - - - +
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Residues in contact with PHE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C ARG* 3.7 53.8 - - + -
92C THR* 1.3 74.7 - - - +
94C GLY* 1.3 62.2 + - - +
95C ALA 3.8 0.3 + - - -
96C PHE* 3.7 26.8 + + + -
142C GLN* 3.5 2.6 - - - -
143C LEU* 2.8 39.3 + - + +
145C VAL* 3.8 28.0 - - + -
156C PHE* 4.8 7.0 - + - -
159C ILE* 4.1 9.6 - - + -
160C ALA* 4.0 28.7 - - + -
163C ALA* 3.5 25.8 - - + -
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Residues in contact with GLY 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C THR 4.3 1.0 + - - -
93C PHE* 1.3 70.3 - - - +
95C ALA* 1.3 72.9 + - - +
96C PHE* 3.2 5.7 + - - +
133C LEU* 5.7 0.7 - - - -
140C ILE* 4.4 3.1 - - - -
141C PRO 3.5 0.2 - - - -
142C GLN* 3.4 25.7 + - - -
21D PRO* 4.6 6.1 - - - +
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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