Contacts of the strand formed by residues 111 - 117 (chain I) in PDB entry 1VYJ
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 111 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102I VAL* 3.9 17.7 - - + -
103I PHE 3.4 4.3 - - - -
104I GLU* 4.0 21.5 - - + +
109I GLU* 5.2 11.7 - - + +
110I LYS* 1.3 75.3 - - - +
112I SER* 1.3 63.5 - - - +
113I ASP* 3.7 21.9 + - - +
179K ASN 4.0 0.3 - - - +
180K ILE* 3.8 0.7 - - - -
181K LYS* 3.0 41.6 + - + +
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Residues in contact with SER 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81I CYS 4.7 4.3 + - - -
101I LEU 3.4 3.3 - - - +
102I VAL* 3.3 5.7 - - - +
103I PHE* 2.8 53.8 + - - -
110I LYS* 3.3 13.2 + - - -
111I VAL* 1.3 73.7 - - - +
113I ASP* 1.3 62.1 + - - +
114I TYR* 3.7 21.8 + - - -
179K ASN 3.4 4.5 - - - -
180K ILE* 3.5 24.8 - - - +
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Residues in contact with ASP 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I ARG* 5.4 1.2 + - - -
100I ALA* 5.5 3.1 - - - +
101I LEU 3.9 0.9 - - - -
102I VAL* 3.5 23.9 - - - +
111I VAL* 3.7 22.0 + - - +
112I SER* 1.3 70.5 - - - +
114I TYR* 1.3 63.8 + - - +
177K ASN* 4.2 1.7 - - - +
178K GLY* 3.7 1.6 - - - -
179K ASN* 2.6 52.5 + - + +
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Residues in contact with TYR 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I ILE* 3.7 24.7 - - + -
81I CYS* 3.1 38.6 + - + +
100I ALA* 3.5 6.6 - - - +
101I LEU* 2.8 38.3 + - + +
103I PHE* 3.7 20.0 - + - -
112I SER* 3.7 25.4 - - - -
113I ASP* 1.3 81.3 - - - +
115I GLU* 1.3 62.2 + - - +
150K ASP* 4.4 0.5 - - - +
151K LEU* 3.9 4.9 - - + +
154K ILE* 3.6 33.7 - - + -
177K ASN 3.6 2.7 - - - -
178K GLY* 3.8 21.8 - - - -
180K ILE* 3.6 26.1 - - + +
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Residues in contact with GLU 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I ILE* 4.7 3.9 - - - +
98I THR* 3.1 31.4 + - - +
99I LEU 3.8 4.3 - - - +
100I ALA* 4.6 9.6 + - - +
114I TYR* 1.3 77.7 - - - +
116I MET* 1.3 60.1 + - - +
117I LYS* 6.4 0.9 - - + -
176K GLY* 2.9 26.4 - - - -
177K ASN* 2.8 47.7 + - - +
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Residues in contact with MET 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I VAL* 3.8 20.2 - - + -
71I ASN 4.5 3.8 - - - +
74I SER* 4.1 13.0 - - - +
75I MET* 3.5 52.9 - - + -
78I ILE* 3.8 17.2 - - + +
98I THR* 3.0 7.4 - - - -
99I LEU* 2.9 61.5 + - + +
101I LEU* 4.5 4.2 - - + +
115I GLU* 1.3 75.1 - - - +
117I LYS* 1.3 75.6 + - - +
118I LEU* 3.5 4.1 + - + +
175K LEU* 3.6 9.9 - - + +
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Residues in contact with LYS 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I GLY 4.4 1.4 - - - +
71I ASN* 5.3 6.1 + - - +
74I SER* 5.9 0.7 - - - -
97I ASP 4.0 4.9 - - - +
98I THR* 4.4 4.3 - - - +
115I GLU* 6.4 0.4 - - + -
116I MET* 1.3 85.9 - - - +
118I LEU* 1.3 68.0 + - - +
119I MET* 5.8 1.4 - - - +
173K GLY 4.0 4.8 + - - -
174K GLU* 3.0 37.0 + - - +
175K LEU* 2.9 19.2 + - - +
176K GLY* 3.8 13.7 - - - +
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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