Contacts of the strand formed by residues 18 - 25 (chain I) in PDB entry 1V7M
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 MET 18 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8I GLY 3.3 28.7 - - - +
9I GLY* 3.9 15.7 - - - +
10I GLY 3.4 23.3 - - - +
11I LEU 3.6 15.7 - - - +
12I VAL* 3.6 23.1 - - + -
17I SER* 1.3 79.6 + - - +
19I LYS* 1.3 63.2 + - - +
20I LEU* 4.1 2.2 - - + -
83I LEU 3.7 0.9 - - - +
84I GLN* 4.0 4.6 + - - -
85I MET* 2.9 51.7 + - + +
88I LEU* 4.3 1.6 - - + -
112I VAL* 4.1 7.9 - - - -
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Residues in contact with LYS 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I GLY* 3.5 21.0 - - - +
18I MET* 1.3 75.3 - - - +
20I LEU* 1.3 73.3 + - - +
21I SER* 4.2 10.2 + - - +
73I SER* 5.0 3.4 + - - -
82I TYR* 3.9 30.2 - - - +
83I LEU 3.3 7.4 - - - +
84I GLN* 3.7 31.3 + - - +
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Residues in contact with LEU 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I GLU* 6.1 0.7 - - + -
7I SER 3.7 4.5 - - - +
8I GLY* 3.4 33.4 - - - +
9I GLY* 3.8 8.3 - - - +
18I MET* 4.1 9.2 - - + -
19I LYS* 1.3 75.8 - - - +
21I SER* 1.3 62.4 + - - +
36I TRP* 3.9 19.9 - - + -
81I VAL 4.0 0.2 - - - +
82I TYR* 3.3 8.3 - - - +
83I LEU* 2.8 46.4 + - + +
85I MET* 4.4 8.7 - - + -
96I TYR* 3.7 41.5 - - + -
110I THR* 5.0 9.0 - - - +
112I VAL* 4.1 10.5 - - + -
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Residues in contact with SER 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I GLU 4.4 0.2 - - - -
6I GLU* 3.3 7.8 - - - +
7I SER* 3.0 43.6 + - - +
8I GLY* 4.9 0.2 - - - -
19I LYS* 4.2 9.8 + - - +
20I LEU* 1.3 74.1 - - - +
22I CYS* 1.3 65.2 + - - +
23I ALA 5.4 0.2 - - - -
36I TRP* 4.0 4.3 - - - -
81I VAL 3.6 4.9 - - - -
82I TYR* 3.3 25.6 - - - -
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Residues in contact with CYS 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I LEU* 4.1 21.8 - - - -
5I GLU 3.2 12.1 - - - +
6I GLU* 4.7 0.2 - - - -
21I SER* 1.3 79.4 - - - +
23I ALA* 1.3 63.1 + - - +
24I ALA* 3.8 0.6 + - - +
29I PHE* 5.5 0.7 - - - -
34I MET* 4.6 0.2 - - - -
36I TRP* 4.1 2.9 - - + -
79I SER 3.7 0.2 - - - +
80I SER* 3.1 28.4 - - - -
81I VAL* 2.9 23.8 + - + -
82I TYR* 4.7 0.2 - - - -
98I CYS* 2.0 52.3 - - + -
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Residues in contact with ALA 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I LYS* 3.5 1.7 - - - +
4I LEU* 3.4 5.0 - - - -
5I GLU* 2.9 38.2 + - + +
22I CYS* 1.3 73.7 - - - +
24I ALA* 1.3 61.9 + - - +
25I SER 4.1 0.2 + - - -
78I LYS 5.8 0.7 - - - +
79I SER 3.7 3.8 - - - -
80I SER* 4.4 5.6 - - - +
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Residues in contact with ALA 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I LYS 3.4 4.3 - - - -
4I LEU* 3.6 21.1 - - + -
22I CYS* 3.8 0.8 + - - +
23I ALA* 1.3 74.8 - - - +
25I SER* 1.3 61.0 + - - +
27I PHE* 3.6 12.1 - - + +
29I PHE* 3.4 35.7 - - + -
79I SER* 2.7 33.1 + - - +
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Residues in contact with SER 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I GLU 4.9 0.7 + - - -
2I VAL* 3.5 3.5 - - - -
3I LYS* 2.9 57.1 + - - +
23I ALA 4.1 0.4 + - - -
24I ALA* 1.3 74.5 - - - +
26I GLY* 1.3 61.3 + - - +
27I PHE* 3.6 8.8 + - - -
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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