Contacts of the strand formed by residues 71 - 78 (chain C) in PDB entry 1VF5
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 ASN 71 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C GLY 4.7 5.3 + - - -
70C LEU* 1.3 78.3 + - - +
72C VAL* 1.3 62.1 + - - +
119C LEU* 2.6 29.5 - - + +
120C PRO 3.2 9.7 - - - +
121C GLY* 3.7 4.3 + - - -
155C ARG* 3.3 16.9 - - - -
156C GLY 3.6 3.1 + - - -
301C HEM 3.3 48.4 + - + +
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Residues in contact with VAL 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ILE* 4.2 17.7 - - + +
70C LEU* 5.3 2.2 - - + -
71C ASN* 1.3 74.9 - - - +
73C GLY* 1.3 58.5 + - - +
119C LEU* 3.0 27.4 - - - -
120C PRO* 2.8 24.7 + - + +
121C GLY 3.9 12.6 - - - +
124C TYR* 3.3 33.7 - - + +
125C GLN* 4.1 12.6 - - - +
127C ILE* 3.6 16.6 - - + -
154C ASN 3.7 13.7 - - - +
155C ARG* 4.3 6.7 - - + -
301C HEM 3.3 7.5 - - - +
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Residues in contact with GLY 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C PRO* 4.5 1.3 - - - -
52C ILE* 3.0 16.4 - - - +
72C VAL* 1.3 76.3 - - - +
74C ALA* 1.3 65.8 + - - +
116C VAL* 4.2 15.0 - - - -
118C PRO 4.9 0.2 - - - -
119C LEU* 5.2 0.2 - - - -
127C ILE* 5.3 0.4 - - - -
154C ASN 3.1 16.0 + - - -
301C HEM 3.4 25.8 - - - +
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Residues in contact with ALA 74 (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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2C PRO* 4.2 1.0 - - - +
50C VAL* 4.2 14.8 - - + -
52C ILE* 4.0 13.2 - - + -
73C GLY* 1.3 76.9 - - - +
75C VAL* 1.3 64.0 + - - +
115C LEU* 3.9 6.8 - - - +
116C VAL* 3.3 37.8 + - + +
127C ILE* 5.2 2.0 - - + -
129C PHE* 5.3 2.7 - - + -
151C LEU* 4.3 3.8 - - + -
152C GLY 3.1 14.4 - - - +
153C ALA* 4.2 0.9 - - - -
301C HEM 3.0 16.4 - - - +
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Residues in contact with VAL 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PRO* 4.0 28.7 - - + -
20C ILE* 3.7 24.0 - - + -
22C CYS* 5.0 0.4 - - - -
74C ALA* 1.3 77.3 - - - +
76C LEU* 1.3 66.5 + - - +
77C MET* 4.7 6.5 - - + -
106C TYR* 4.9 0.4 - - + -
113C VAL* 4.9 4.0 - - + -
114C LEU 3.6 8.5 - - - +
115C LEU* 4.0 19.1 - - + -
129C PHE* 6.0 0.2 - - - -
150C HIS 3.9 0.5 - - - +
151C LEU* 3.3 9.5 - - - +
152C GLY* 3.0 39.9 + - - +
301C HEM 4.3 8.1 - - + -
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Residues in contact with LEU 76 (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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34C VAL* 4.2 10.8 - - + -
48C ALA* 4.8 7.9 - - + -
50C VAL* 3.5 24.0 - - + -
75C VAL* 1.3 75.3 - - - +
77C MET* 1.3 66.1 + - - +
78C LEU* 3.5 20.0 - - + -
112C ASN 3.8 1.0 - - - +
113C VAL* 3.2 5.9 - - - +
114C LEU* 2.9 36.5 + - + +
129C PHE* 3.5 42.1 - - + -
149C ILE* 3.8 20.9 - - + -
150C HIS 3.1 20.6 - - - +
151C LEU* 4.4 6.5 - - + -
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Residues in contact with MET 77 (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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12C THR* 4.5 2.7 - - - +
13C PRO* 3.7 27.4 - - + -
14C ARG* 3.4 39.3 - - + -
20C ILE* 4.4 6.3 - - - -
75C VAL* 4.7 5.8 - - + -
76C LEU* 1.3 77.6 - - - +
78C LEU* 1.3 65.2 + - - +
112C ASN 3.7 3.6 - - - -
113C VAL* 3.9 21.8 - - + +
148C ALA 4.1 1.2 - - - +
149C ILE* 3.2 9.9 - - - +
150C HIS* 3.1 58.4 + - + +
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Residues in contact with LEU 78 (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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36C VAL* 6.2 0.7 - - + -
48C ALA* 5.5 3.4 - - + -
76C LEU* 3.5 35.2 - - + +
77C MET* 1.3 76.4 - - - +
79C PRO* 1.3 74.0 - - + +
82C PHE* 3.7 17.9 - - + -
83C LYS* 4.4 7.4 - - - +
84C ILE* 5.6 0.2 - - + -
112C ASN* 2.6 39.7 + - - +
114C LEU* 4.4 19.3 - - + -
129C PHE* 5.8 1.3 - - + -
131C VAL* 3.8 39.7 - - + -
148C ALA 4.5 0.9 - - - -
149C ILE* 4.5 11.4 - - + -
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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