Contacts of the strand formed by residues 113 - 118 (chain A) in PDB entry 3VKO
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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110A LEU* 2.8 56.8 + - + +
112A ASP* 1.3 84.7 - - + +
114A PHE* 1.3 65.6 + - - +
115A GLN* 5.1 1.3 - - - -
125A LEU* 3.8 36.4 - - + +
126A TYR 3.2 17.7 - - - +
127A GLY* 3.5 7.9 - - - +
128A HIS* 3.1 15.7 + - - -
204A CL 4.5 8.5 - - + -
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Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.8 0.7 - - + -
50A LEU* 3.5 20.2 - - + -
63A ALA* 4.8 6.5 - - + -
64A PHE* 3.5 49.6 - + + -
107A ILE* 3.9 19.5 - - + -
108A MET 3.3 2.9 - - - +
109A VAL* 3.9 24.5 - - + -
113A LYS* 1.3 75.1 - - - +
115A GLN* 1.3 59.8 - - - +
116A VAL* 4.2 1.7 - - + +
125A LEU* 3.5 7.3 - - - +
126A TYR* 2.9 41.4 + + + +
128A HIS* 3.4 32.3 - + - -
130A ILE 5.9 0.7 - - - -
132A PRO* 4.6 0.2 - - + -
135A ILE* 3.6 29.2 - - + -
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Residues in contact with GLN 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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106A VAL 3.6 1.2 - - - +
107A ILE* 3.5 1.2 - - - -
108A MET* 2.7 68.3 + - + +
110A LEU* 3.7 23.6 - - + +
113A LYS* 5.1 1.0 - - - -
114A PHE* 1.3 74.1 - - - +
116A VAL* 1.3 62.7 + - - +
117A ALA* 6.3 0.6 - - + +
122A HIS* 3.8 19.9 + - + +
124A LEU 3.7 3.1 - - - -
125A LEU* 3.3 24.1 - - + +
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 4.0 22.9 - - + -
66A PHE* 3.7 26.9 - - + -
105A ILE* 4.0 16.4 - - + -
106A VAL 3.4 6.7 - - - +
107A ILE* 4.0 18.4 - - + -
114A PHE* 4.9 0.4 - - + -
115A GLN* 1.3 81.4 - - - +
117A ALA* 1.3 61.7 + - - +
118A VAL* 4.4 4.0 - - + -
122A HIS* 3.8 4.7 + - - -
123A THR* 2.8 31.1 + - - -
124A LEU* 2.9 35.7 + - + +
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Residues in contact with ALA 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 GLU 3.8 0.9 - - - +
106A VAL* 2.9 42.6 + - + +
115A GLN* 4.3 1.1 + - + +
116A VAL* 1.3 75.7 - - - +
118A VAL* 1.3 65.3 + - - +
120A GLY* 4.7 7.0 - - - +
121A LYS 3.3 24.0 - - - +
122A HIS* 3.9 6.3 - - - +
123A THR* 3.9 0.2 - - - -
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Residues in contact with VAL 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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96A PRO* 3.8 20.7 - - + +
97A PHE* 3.7 41.1 - - + -
103A PHE* 4.3 3.4 - - + -
104A GLU 3.4 7.6 - - - +
105A ILE* 4.4 5.2 - - + -
116A VAL* 4.4 10.3 - - + -
117A ALA* 1.3 76.4 - - - +
119A ASN* 1.3 94.9 + - - +
120A GLY 3.1 0.9 - - - -
121A LYS* 2.9 23.1 + - - +
123A THR* 3.3 21.9 + - + +
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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