Contacts of the strand formed by residues 23 - 31 (chain A) in PDB entry 1VI7
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 SER 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A GLU 3.8 0.2 - - - +
19A GLU* 3.4 4.0 - - - +
20A ILE 3.0 22.0 + - - -
21A LYS 2.7 14.7 + - - -
22A LYS* 1.3 74.3 - - - +
24A ARG* 1.3 78.9 + - - +
25A PHE* 4.1 14.8 - - - -
104A ARG* 4.2 12.7 + - - -
105A TYR 3.4 13.5 - - - -
107A GLY* 3.1 15.6 + - - +
109A ILE 3.7 10.7 + - - -
111A LEU* 4.6 0.9 - - - +
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Residues in contact with ARG 24 (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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17A VAL* 3.6 32.9 - - + +
18A GLU 2.7 30.8 + - - -
19A GLU* 3.1 31.6 + - - +
23A SER* 1.3 96.4 + - - +
25A PHE* 1.3 62.5 + - - +
26A ILE* 3.9 2.4 + - + +
103A VAL 2.9 15.8 - - - +
105A TYR* 2.7 54.2 + - + -
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Residues in contact with PHE 25 (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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17A VAL* 3.3 2.7 - - - -
18A GLU* 2.8 48.7 + - + +
20A ILE* 3.5 43.5 - - + -
23A SER* 4.1 11.2 - - - -
24A ARG* 1.3 73.0 - - - +
26A ILE* 1.3 60.0 + - - +
27A THR* 4.0 3.7 + - - +
102A VAL* 4.2 15.7 - - + -
103A VAL 3.4 4.0 - - - -
104A ARG* 3.3 54.5 - - + -
111A LEU* 5.1 5.4 - - + -
116A LEU* 5.1 2.5 - - + -
119A ALA* 3.7 31.4 - - + +
120A TYR* 4.0 17.5 - + - -
123A GLY* 6.5 0.2 - - - -
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Residues in contact with ILE 26 (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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15A THR* 5.7 1.3 - - - +
16A VAL 3.3 6.1 - - - +
17A VAL* 3.4 24.2 - - + -
24A ARG* 3.9 4.2 + - + +
25A PHE* 1.3 71.1 - - - +
27A THR* 1.3 63.4 + - - +
28A MET* 3.8 10.2 + - + +
49A HIS* 5.1 11.7 - - + -
101A VAL 3.2 10.9 - - - +
102A VAL* 4.4 0.7 - - - -
103A VAL* 3.3 38.3 + - + +
105A TYR* 5.9 2.5 - - + -
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Residues in contact with THR 27 (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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14A VAL 4.1 0.2 - - - +
15A THR* 3.4 0.2 - - - -
16A VAL* 2.8 38.7 + - - +
25A PHE* 4.0 2.6 + - - +
26A ILE* 1.3 72.2 - - - +
28A MET* 1.3 67.7 + - - +
29A LEU* 3.8 22.7 - - + -
100A ALA* 4.9 0.7 - - + -
101A VAL 3.3 6.7 - - - +
102A VAL* 4.0 17.0 - - + +
123A GLY* 3.4 43.8 + - - +
124A VAL* 4.0 13.2 - - + +
127A ALA* 4.0 6.1 - - + -
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Residues in contact with MET 28 (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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14A VAL 3.2 7.2 - - - +
15A THR* 3.8 21.1 - - - +
26A ILE* 4.0 14.4 - - + +
27A THR* 1.3 81.0 - - - +
29A LEU* 1.3 65.2 + - - +
41A PHE* 4.1 18.0 - - + -
45A VAL* 4.4 22.9 - - + +
48A GLU* 4.3 13.2 - - - +
49A HIS* 4.3 21.1 - - - -
99A THR 4.0 0.2 - - - +
100A ALA* 3.4 3.5 - - - -
101A VAL* 3.0 36.0 + - + +
103A VAL* 5.0 2.9 - - - -
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Residues in contact with LEU 29 (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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13A PRO* 3.7 3.5 - - - +
14A VAL* 2.7 38.0 + - + +
27A THR* 3.8 12.1 - - + -
28A MET* 1.3 80.9 - - - +
30A ALA* 1.3 67.6 + - - +
41A PHE* 4.5 1.1 - - - -
90A LEU* 5.2 0.2 - - + -
98A ILE* 3.9 17.9 - - + -
99A THR 3.6 7.0 - - - +
100A ALA* 4.0 12.6 - - + -
124A VAL* 4.6 5.8 - - + -
127A ALA* 3.4 37.2 - - + +
128A LEU* 3.4 36.1 - - + +
131A LEU* 4.3 11.9 - - + -
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Residues in contact with ALA 30 (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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10A PRO* 4.2 7.5 - - - +
12A ALA 5.0 1.5 + - - -
13A PRO* 4.0 20.6 - - + +
29A LEU* 1.3 81.0 - - - +
31A HIS* 1.3 66.1 + - - +
32A THR* 3.5 3.8 + - - +
41A PHE* 3.8 29.8 - - + -
98A ILE* 3.8 6.6 - - - +
99A THR 3.5 20.8 + - - +
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Residues in contact with HIS 31 (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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9A ILE* 3.4 29.4 - - + +
10A PRO* 3.5 28.1 - - + +
12A ALA 5.3 1.5 + - - +
13A PRO* 5.2 2.2 - - - +
30A ALA* 1.3 73.8 - - - +
32A THR* 1.3 64.2 + - - +
33A ASP* 4.1 19.4 + - + +
37A ALA* 5.3 0.3 - - - +
97A GLU* 3.0 34.9 + - - -
136A LYS* 5.5 1.0 - - - +
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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