Contacts of the strand formed by residues 111 - 117 (chain A) in PDB entry 2VTX
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 LEU 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A CYS 3.9 0.2 - - - +
22A GLU* 3.4 2.9 - - - -
23A LEU* 2.8 52.3 + - + +
50A VAL* 3.6 32.3 - - + -
51A CYS 3.6 5.2 - - - +
52A LEU* 4.0 19.5 - - + -
61A HIS* 4.0 12.3 - - + -
63A VAL* 4.4 12.6 - - + -
81A LEU* 4.4 4.5 - - + -
104A LEU* 3.9 26.9 - - + -
109A GLY* 4.7 2.5 - - - -
110A PRO* 1.3 74.6 - - - +
112A TYR* 1.3 61.9 + - - +
113A ILE* 3.7 22.0 - - + -
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Residues in contact with TYR 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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21A CYS 3.4 5.6 - - - +
22A GLU* 3.6 37.6 + - + -
49A THR 4.2 0.2 - - - +
50A VAL* 3.2 6.9 - - - +
51A CYS* 2.7 52.7 + - - +
52A LEU 4.1 2.2 - - - -
53A GLY* 3.6 29.2 - - - -
110A PRO* 3.8 18.0 - - + +
111A LEU* 1.3 74.6 - - - +
113A ILE* 1.3 61.3 + - - +
62B ILE* 4.8 6.5 - - + -
77B PRO* 3.7 52.5 - - + +
105B LYS* 3.7 22.4 + - - -
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Residues in contact with ILE 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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19A TRP* 3.9 13.7 - - + -
20A GLY* 3.1 22.0 - - - -
21A CYS* 3.0 25.2 + - - +
23A LEU* 4.1 7.4 - - + -
47A LEU* 4.2 17.7 - - + -
49A THR 3.6 7.6 - - - +
50A VAL* 4.4 11.4 - - + +
63A VAL* 4.0 15.9 - - + -
78A ILE* 5.9 0.7 - - + -
102A PHE* 3.6 40.4 - - + -
111A LEU* 3.7 13.7 - - + -
112A TYR* 1.3 76.8 - - - +
114A SER* 1.3 70.5 + - - +
76B VAL* 4.7 0.7 - - - +
77B PRO 4.8 2.6 - - - +
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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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18A ILE* 4.9 3.6 - - - -
19A TRP* 3.3 8.3 - - - -
47A LEU* 3.6 4.7 - - - -
48A ARG* 2.8 26.3 + - - +
49A THR* 2.7 41.2 + - - +
113A ILE* 1.3 80.2 - - - +
115A GLY* 1.4 59.0 + - - +
76B VAL* 3.6 22.7 - - - -
77B PRO 3.7 10.5 - - - -
78B ILE* 4.1 9.2 - - - +
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Residues in contact with GLY 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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18A ILE* 3.6 3.0 - - - +
19A TRP* 2.7 54.0 + - - +
45A LEU* 4.2 2.2 - - - -
46A ALA 3.0 14.1 - - - -
47A LEU* 4.0 1.8 - - - -
48A ARG* 3.9 6.5 - - - +
114A SER* 1.4 75.7 - - - +
116A GLN* 1.3 65.4 + - - +
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ASP* 3.1 27.0 + - - +
17A LEU 4.0 4.7 - - - +
18A ILE* 3.9 14.6 - - + +
19A TRP* 4.8 0.4 - - - +
45A LEU* 3.7 7.2 - - - +
46A ALA 2.8 32.3 + - - -
48A ARG* 3.0 38.2 + - + +
115A GLY* 1.3 79.2 - - - +
117A HIS* 1.3 63.0 + - - +
118A VAL* 3.5 7.5 - - + +
93B GLY 3.2 12.3 - - - +
94B ILE* 3.5 4.0 - - - -
95B GLU* 2.8 33.0 + - - +
96B LEU* 4.1 10.7 - - - +
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Residues in contact with HIS 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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16A ASP 3.4 21.6 + - - +
17A LEU* 3.5 37.3 + - + +
18A ILE 5.4 0.4 + - - -
19A TRP* 4.1 22.4 - + + +
32A PHE* 3.8 35.0 - + - -
34A VAL* 5.7 5.9 - - + +
43A HIS* 4.6 21.0 - + + +
44A GLN 3.5 8.8 + - - +
45A LEU* 4.5 3.3 - - + +
116A GLN* 1.3 68.1 - - - +
118A VAL* 1.3 70.7 + - - +
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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