Contacts of the strand formed by residues 71 - 78 (chain C) in PDB entry 1VCB
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 PRO 71 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C ARG 3.2 11.9 - - - +
70C GLU* 1.3 85.4 - - + +
72C SER* 1.3 60.0 + - - +
73C GLN 4.3 0.4 - - - -
110C HIS* 6.5 1.3 - - + -
111C SER 3.6 3.1 - - - +
112C TYR* 3.6 20.0 - - + -
113C ARG* 4.6 4.9 - - - +
141C ASN* 4.3 8.0 + - - +
142C VAL* 5.6 3.6 - - - +
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Residues in contact with SER 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C GLU 3.5 0.2 + - - -
71C PRO* 1.3 76.0 - - - +
73C GLN* 1.3 63.1 + - - +
74C VAL* 3.6 2.4 + - - +
110C HIS* 5.1 0.7 - - - -
111C SER* 2.9 32.3 + - - -
112C TYR* 3.7 5.6 - - - -
113C ARG* 3.7 21.3 - - - -
138C PRO* 3.5 16.7 - - - +
139C SER 2.8 26.9 + - - -
141C ASN* 3.8 9.9 + - - -
147C ILE* 4.2 4.0 - - - +
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Residues in contact with GLN 73 (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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71C PRO 4.3 0.4 - - - -
72C SER* 1.3 71.6 - - - +
74C VAL* 1.3 63.3 + - - +
108C ARG* 2.9 45.9 + - + +
109C ILE 3.7 11.0 - - - +
110C HIS* 3.4 24.1 + - + +
141C ASN* 2.5 40.2 + - - +
145C GLN* 4.4 13.3 + - - +
146C PRO* 3.5 16.2 - - + +
147C ILE* 3.0 14.1 + - - +
111K ASP* 4.3 13.6 + - - +
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Residues in contact with VAL 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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72C SER* 3.9 9.0 - - - +
73C GLN* 1.3 78.1 - - - +
75C ILE* 1.3 71.8 + - - +
76C PHE* 3.8 21.1 - - + -
108C ARG* 3.5 5.9 - - - +
109C ILE* 2.6 47.4 + - + +
111C SER* 4.2 5.6 - - - -
136C PHE* 3.3 27.8 - - + -
138C PRO* 3.7 36.8 - - + -
146C PRO* 5.3 1.6 - - - -
147C ILE* 3.4 15.7 - - + +
149C ALA* 4.1 0.9 - - + -
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Residues in contact with ILE 75 (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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74C VAL* 1.3 80.0 - - - +
76C PHE* 1.3 68.0 + - - +
77C CYS* 3.4 4.9 + - + +
106C GLY* 5.4 0.4 - - - -
107C ARG 3.5 13.7 - - - +
108C ARG* 4.8 5.2 - - + +
146C PRO* 4.4 12.8 - - + -
147C ILE 2.9 17.4 + - - +
148C PHE* 3.2 50.3 - - + -
149C ALA* 2.8 29.3 + - - +
41K THR* 3.4 35.4 - - + +
45K MET* 4.2 2.0 - - + -
109K PHE* 4.6 9.0 - - + -
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Residues in contact with PHE 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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74C VAL* 3.8 20.2 - - + -
75C ILE* 1.3 74.7 - - - +
77C CYS* 1.3 61.0 + - - +
78C ASN 3.5 1.0 + - - -
86C PRO* 3.7 28.0 - - + -
98C TYR* 5.6 0.9 - + + -
101C LEU* 3.7 24.2 - - + +
106C GLY* 3.0 20.4 - - - -
107C ARG* 2.8 21.2 + - + +
109C ILE* 3.5 30.5 - - + -
117C TRP* 3.7 39.0 - + - -
119C PHE* 3.7 24.2 - + - -
136C PHE* 4.4 5.6 - + - -
149C ALA* 3.8 15.9 - - + -
151C ILE* 4.3 2.9 - - + -
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Residues in contact with CYS 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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75C ILE* 3.4 4.5 + - + -
76C PHE* 1.3 72.2 - - - +
78C ASN* 1.3 61.8 + - - +
79C ARG* 3.3 25.3 + - - +
104C GLY 5.3 3.8 - - - -
105C THR 4.5 2.9 - - - -
106C GLY* 4.0 13.7 - - - -
148C PHE* 3.5 25.1 - - + -
149C ALA 3.0 9.8 + - - +
150C ASN* 3.7 3.4 - - - +
151C ILE* 3.0 27.8 + - - +
45K MET* 3.7 28.5 - - - -
63K ARG* 5.7 5.2 - - - -
109K PHE* 5.9 0.2 - - - -
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Residues in contact with ASN 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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76C PHE 3.5 1.8 + - - -
77C CYS* 1.3 71.6 - - - +
79C ARG* 1.3 56.5 + - - +
80C SER* 2.9 27.9 + - - -
82C ARG 3.0 19.4 + - - -
84C VAL* 3.3 15.0 - - + +
101C LEU* 3.5 23.2 + - + -
102C PRO 2.8 27.0 + - - +
103C PRO 3.4 15.7 - - - +
104C GLY* 3.6 14.1 - - - +
105C THR 2.9 19.3 + - - +
151C ILE* 4.1 7.4 - - + +
63K ARG* 5.9 0.5 + - - -
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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