Contacts of the strand formed by residues 113 - 121 (chain A) in PDB entry 2VCK
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 LYS 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A PHE* 3.0 34.6 + - + +
110A SER* 3.4 21.3 + - - +
112A LYS* 1.3 83.3 - - + +
114A VAL* 1.3 77.5 + - - +
158A TYR* 3.6 34.2 - - + +
159A CYS* 3.7 13.3 + - - +
161A PRO* 4.2 1.0 - - - +
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Residues in contact with VAL 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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23A ILE* 4.2 4.0 - - + -
24A TRP* 4.1 9.4 - - + -
107A MSE 3.2 12.3 - - - +
108A LYS* 4.1 13.9 - - + -
109A PHE* 5.7 0.9 - - - -
113A LYS* 1.3 88.6 - - - +
115A ILE* 1.3 63.4 + - - +
116A ILE* 4.4 4.0 - - + -
158A TYR* 3.3 5.5 - - - +
159A CYS* 2.8 59.1 + - - +
161A PRO* 3.7 37.2 - - + -
164A VAL* 3.6 13.0 - - + -
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Residues in contact with ILE 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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24A TRP* 4.3 0.7 - - - -
105A ASP 3.8 0.9 - - - +
106A LEU* 3.8 1.2 - - - -
107A MSE 2.8 73.8 + - + +
109A PHE* 3.9 12.3 - - + -
114A VAL* 1.3 75.2 - - - +
116A ILE* 1.3 65.8 + - - +
117A VAL* 3.7 13.2 - - + -
156A VAL* 4.1 3.6 - - + -
157A ARG 3.3 9.9 - - - +
158A TYR* 3.6 17.9 - - + -
1234A BLA 3.2 51.8 - - + +
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Residues in contact with ILE 116 (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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24A TRP* 3.7 24.9 - - + -
27A TYR* 3.5 24.7 - - + +
105A ASP 4.1 1.3 - - - -
106A LEU* 4.1 9.2 - - + -
114A VAL* 4.4 3.1 - - + -
115A ILE* 1.3 71.9 - - - +
117A VAL* 1.3 63.7 + - - +
118A PHE* 3.7 33.2 - - + -
155A PHE* 4.4 8.1 - - + -
156A VAL* 3.2 6.2 - - - +
157A ARG* 2.9 37.7 + - + +
159A CYS* 4.5 5.4 - - - -
164A VAL* 4.0 22.2 - - + +
167A TYR* 3.9 21.1 - - + -
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Residues in contact with VAL 117 (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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104A MSE 3.3 2.4 - - - +
105A ASP* 2.9 40.9 + - + +
106A LEU* 3.8 3.0 - - - +
107A MSE 3.6 24.5 - - + -
115A ILE* 3.7 14.6 - - + -
116A ILE* 1.3 81.0 - - - +
118A PHE* 1.3 70.4 + - - +
154A ILE* 4.3 7.9 - - + -
155A PHE 3.1 7.6 - - - +
156A VAL* 3.8 13.7 - - + -
1234A BLA 3.7 47.3 - - + -
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Residues in contact with PHE 118 (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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27A TYR* 4.5 3.6 - + - -
102A PHE* 4.2 9.6 - + + -
103A GLY 3.2 13.0 - - - +
104A MSE 4.0 9.6 - - + +
106A LEU* 4.8 3.1 - - + -
116A ILE* 3.7 22.7 - - + -
117A VAL* 1.3 75.9 - - - +
119A ASP* 1.3 65.4 + - - +
153A ASN 4.4 0.7 - - - +
154A ILE* 4.3 0.3 - - - +
155A PHE* 2.9 71.5 + + + +
167A TYR 4.6 2.2 - - - -
170A THR* 4.3 2.7 - - + -
171A PHE* 3.6 51.4 - + + -
174A TYR* 3.6 39.9 - + - -
1234A BLA 4.3 1.6 - - - -
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Residues in contact with ASP 119 (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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102A PHE* 3.3 13.6 - - - -
103A GLY* 2.9 33.0 + - - -
118A PHE* 1.3 78.9 - - - +
120A PHE* 1.3 78.4 + - - +
121A GLN* 3.7 5.4 + - + +
150A PHE* 3.1 24.8 - - + +
151A SER* 2.5 49.7 + - - -
153A ASN 3.7 1.7 - - - +
154A ILE* 3.4 26.3 + - + +
174A TYR* 4.9 4.7 - - - -
1234A BLA 4.4 3.1 - - + +
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Residues in contact with PHE 120 (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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100A PRO* 4.1 11.4 - - + -
101A CYS 3.4 2.9 - - - -
102A PHE* 4.0 10.3 - + - -
119A ASP* 1.3 86.5 + - - +
121A GLN* 1.3 60.7 + - - +
122A HIS 3.8 2.5 + - - -
129A PHE* 3.7 23.1 - + + +
131A VAL* 3.8 15.3 - - + -
134A LEU* 3.5 29.6 - - + -
151A SER* 3.4 26.4 + - - -
153A ASN* 4.9 2.5 - - - -
174A TYR* 3.5 37.0 - + + -
177A LYS* 4.3 4.3 - - + -
178A TYR* 3.7 40.8 - + + -
181A MSE 4.0 15.7 - - + -
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Residues in contact with GLN 121 (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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90A ILE* 4.0 7.8 - - - +
100A PRO* 3.8 2.0 - - - +
101A CYS* 2.8 41.3 + - + +
103A GLY* 3.6 12.9 - - - +
119A ASP* 4.1 12.1 - - + +
120A PHE* 1.3 75.6 - - - +
122A HIS* 1.3 63.2 + - - +
123A PRO* 3.7 1.0 - - - +
149A HIS 3.1 19.6 + - - +
150A PHE* 3.3 36.5 - - + -
198A PHE* 3.5 37.2 - - + -
202A MSE 3.8 8.9 - - - +
1234A BLA 3.6 22.6 - - - +
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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