Contacts of the strand formed by residues 58 - 65 (chain C) in PDB entry 1VCW
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 VAL 58 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ALA 3.8 12.3 - - - +
55C ALA 2.8 7.3 + - - +
56C PRO 4.2 1.9 - - - +
57C ALA* 1.3 78.7 - - - +
59C VAL* 1.3 63.1 + - - +
60C ASN* 6.0 1.1 - - - +
81C SER* 5.7 1.3 - - - -
82C GLY 3.2 8.5 - - - +
83C VAL* 4.6 3.1 - - + +
107C ALA 4.8 0.5 - - - +
108C LEU* 5.3 0.2 - - - -
109C GLN* 3.7 14.3 + - - +
141C ILE* 4.8 0.9 - - + -
158C ILE* 3.4 45.1 - - + +
159C GLY* 4.7 4.7 - - - +
166C GLN* 2.8 38.1 - - + +
203C GLY* 5.4 2.0 - - - -
204C ALA* 4.0 22.2 - - + +
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Residues in contact with VAL 59 (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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56C PRO 5.4 0.2 - - - +
57C ALA 3.7 11.2 - - - +
58C VAL* 1.3 80.5 - - - +
60C ASN* 1.3 74.9 + - - +
61C VAL* 5.2 1.3 - - + -
81C SER* 3.0 9.4 - - - -
82C GLY* 2.5 44.1 + - - +
84C ILE* 3.7 15.7 - - + -
91C ILE* 4.8 4.0 - - + -
106C VAL* 3.2 18.2 - - + -
107C ALA 2.6 41.7 - - - +
108C LEU* 3.3 22.9 - - + -
109C GLN* 5.0 0.4 - - - +
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Residues in contact with ASN 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C VAL* 6.0 1.2 - - - +
59C VAL* 1.3 82.7 + - - +
61C VAL* 1.3 60.6 + - - +
62C TYR* 3.1 36.6 + - + +
80C GLY 3.7 5.2 - - - +
81C SER* 5.4 0.2 - - - -
105C ILE 3.5 2.1 - - - +
106C VAL* 3.4 4.0 - - - -
107C ALA* 3.1 31.5 + - + +
109C GLN* 4.2 17.0 + - - +
160C ASN* 3.0 42.9 + - - +
163C ASN* 4.6 0.7 + - - -
165C GLY* 5.4 2.6 - - - -
166C GLN* 5.2 1.6 + - - +
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Residues in contact with VAL 61 (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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59C VAL* 3.6 2.2 + - + +
60C ASN* 1.3 76.6 - - - +
62C TYR* 1.3 63.5 + - - +
79C LEU* 3.2 5.2 - - - +
80C GLY 2.8 43.2 + - - +
81C SER 3.6 25.6 - - - +
82C GLY* 3.8 8.7 - - - +
91C ILE* 5.2 2.7 - - + -
93C THR* 4.3 6.7 - - - +
97C VAL* 4.5 8.5 - - + -
98C ILE* 3.9 27.6 - - + -
104C ILE* 4.0 14.8 - - + -
105C ILE 3.5 3.1 - - - +
106C VAL* 4.5 12.3 - - + -
130C LEU* 4.1 8.1 - - + -
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Residues in contact with TYR 62 (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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60C ASN* 3.1 40.3 + - + +
61C VAL* 1.3 76.0 - - - +
63C ASN* 1.3 60.9 + - - +
64C ARG* 3.5 8.6 + - + +
76C ILE* 4.4 19.7 - - + -
78C THR 4.1 2.0 - - - -
79C LEU* 3.7 32.3 - - + -
80C GLY 5.7 0.7 - - - -
104C ILE* 3.4 7.8 - - - +
105C ILE* 2.8 57.9 + - + +
107C ALA* 4.2 16.3 - - + +
113C VAL* 6.3 0.2 - - + -
163C ASN* 4.2 14.5 + - - -
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Residues in contact with ASN 63 (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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61C VAL* 4.2 2.0 + - - +
62C TYR* 1.3 71.0 - - - +
64C ARG* 1.3 62.9 + - - +
76C ILE 3.4 1.9 - - - -
77C ARG* 2.8 44.0 + - - +
78C THR* 3.1 27.9 + - - -
79C LEU* 4.3 0.8 - - - +
97C VAL* 3.0 28.1 - - + +
98C ILE* 4.5 3.1 - - + +
99C ASN 2.9 24.8 - - - +
101C ALA* 2.9 32.1 - - + +
103C GLN 3.9 2.7 - - - -
104C ILE* 5.1 1.3 - - - +
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Residues in contact with ARG 64 (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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62C TYR* 3.5 15.5 + - + +
63C ASN* 1.3 80.2 - - - +
65C GLY* 1.3 58.9 + - - +
74C LEU* 3.3 46.3 + - + +
75C GLU 3.0 7.6 - - - +
76C ILE* 3.8 27.2 - - + +
102C ASP* 3.2 2.8 + - - +
103C GLN* 2.7 73.1 + - + +
105C ILE* 4.4 13.2 - - + +
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Residues in contact with GLY 65 (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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64C ARG* 1.3 73.7 - - - +
66C LEU* 1.3 61.4 + - - -
67C ASN 3.6 1.3 - - - -
68C THR* 3.4 7.5 + - - -
73C GLN 3.2 2.1 - - - +
74C LEU* 3.4 3.0 - - - -
75C GLU 2.9 30.6 + - - -
77C ARG* 3.3 27.1 - - - +
102C ASP* 3.5 13.9 - - - -
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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