Contacts of the strand formed by residues 108 - 115 (chain A) in PDB entry 1VCA
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 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A SER* 4.7 2.6 + - - -
106A GLY 4.4 3.6 - - - +
107A LYS* 1.4 88.3 - - + +
109A ILE* 1.3 61.6 + - - +
110A THR* 5.6 0.2 - - - -
157A THR* 4.1 18.6 - - + -
158A PHE 3.6 7.9 - - - +
159A THR* 4.2 10.3 - - - +
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Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 4.2 16.4 - - + -
100A SER* 3.6 17.7 - - - +
101A GLY* 2.9 36.8 - - - +
102A PRO 3.9 11.2 - - - +
103A LEU* 4.6 7.9 - - + +
104A GLU 5.9 0.2 - - - +
107A LYS 3.6 0.8 + - - +
108A PRO* 1.3 75.1 - - - +
110A THR* 1.3 66.5 + - - +
111A VAL* 4.0 0.8 + - + -
156A VAL 3.9 0.9 - - - +
157A THR* 3.2 3.9 - - - -
158A PHE* 2.9 69.0 + - + +
160A PRO* 3.9 16.8 - - + -
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Residues in contact with THR 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A HIS 3.9 0.3 - - - +
99A LEU* 3.6 2.8 - - - -
100A SER* 2.8 47.9 + - - -
108A PRO* 4.3 0.7 - - - +
109A ILE* 1.3 73.4 - - - +
111A VAL* 1.3 67.9 + - - +
112A LYS* 4.2 1.3 + - + +
155A GLU* 4.2 22.0 - - - +
156A VAL 3.4 9.6 - - - +
157A THR* 3.2 22.0 + - - +
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 4.0 20.4 - - + -
98A HIS 3.4 7.6 - - - +
99A LEU* 3.5 20.6 - - + -
109A ILE* 4.5 4.0 - - + -
110A THR* 1.3 73.0 - - - +
112A LYS* 1.3 65.4 + - - +
128A LEU* 4.0 23.3 - - + -
154A LEU* 3.9 1.6 - - - +
155A GLU* 3.3 6.7 - - - +
156A VAL* 2.7 45.7 + - + +
158A PHE* 3.9 27.4 - - + -
169A LEU* 4.1 11.4 - - + -
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Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 3.6 0.9 - - - -
98A HIS* 2.8 67.4 + - + +
110A THR* 4.2 1.9 + - + -
111A VAL* 1.3 75.3 - - - +
113A CYS* 1.3 61.7 + - - +
114A SER* 4.9 5.6 - - - -
153A SER* 3.6 26.2 - - - -
154A LEU 3.5 5.4 - - - +
155A GLU* 3.7 33.5 + - + +
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Residues in contact with CYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A PRO* 3.6 18.4 - - - -
96A GLU 3.3 7.6 - - - +
97A ILE* 4.7 2.7 - - + +
111A VAL* 4.2 1.4 - - + +
112A LYS* 1.3 74.0 - - - +
114A SER* 1.3 62.8 + - - +
115A VAL* 5.2 0.7 - - - -
126A ILE* 4.4 10.2 - - + +
128A LEU* 4.3 11.4 - - + -
153A SER* 3.0 4.2 - - - -
154A LEU* 2.8 44.2 + - + +
171A CYS* 2.0 52.0 - - + -
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ASP 4.8 0.2 - - - +
95A PRO* 3.4 3.2 - - - +
96A GLU* 2.9 34.8 + - - +
98A HIS* 3.3 26.5 - - - -
112A LYS* 4.1 6.7 - - - -
113A CYS* 1.3 74.6 - - - +
115A VAL* 1.3 61.2 + - - +
116A ALA 4.2 0.6 + - - -
151A THR* 4.4 13.9 - - - -
152A LYS 3.2 10.8 - - - -
153A SER* 3.7 10.5 - - - -
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PHE* 4.1 17.3 - - + -
93A LYS 3.8 20.9 - - - +
94A ASP 5.2 0.7 - - - -
95A PRO* 4.4 14.4 - - + -
113A CYS* 5.2 0.4 - - - -
114A SER* 1.3 77.4 - - - +
116A ALA* 1.3 61.6 + - - +
118A VAL* 3.9 21.4 - - + +
124A LEU* 4.4 4.9 - - + -
126A ILE* 3.7 28.9 - - + -
150A GLU 3.9 1.7 - - - +
151A THR* 3.3 4.2 - - - -
152A LYS 2.9 27.1 + - - +
173A ALA* 3.9 20.4 - - + -
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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