Contacts of the strand formed by residues 15 - 22 (chain H) in PDB entry 1OZT
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 GLN 15 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8H LEU* 3.2 16.4 - - - +
9H LYS* 4.8 12.3 - - + -
12H GLY 5.7 0.6 + - - -
13H PRO* 3.6 16.1 + - - +
14H VAL* 1.3 79.7 - - - +
16H GLY* 1.3 59.2 + - - +
35H ILE* 4.1 4.7 - - - -
36H LYS* 2.8 58.6 + - + +
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Residues in contact with GLY 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H VAL* 3.7 3.1 - - - +
8H LEU* 2.8 37.3 + - - +
15H GLN* 1.3 78.0 - - - +
17H ILE* 1.3 68.4 + - - +
34H SER 3.2 15.5 - - - -
35H ILE* 4.0 4.3 - - - -
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Residues in contact with ILE 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G THR* 4.0 31.9 - - + +
5H VAL* 4.0 23.3 - - + -
6H CYS 3.4 4.5 - - - +
7H VAL* 4.7 12.1 - - + -
16H GLY* 1.3 79.5 - - - +
18H ILE* 1.3 66.3 + - - +
19H ASN* 4.3 11.4 - - - +
33H GLY* 3.3 5.7 - - - -
34H SER 3.1 28.3 + - - +
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Residues in contact with ILE 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H VAL* 3.3 5.5 - - - +
6H CYS* 2.9 34.3 + - + +
8H LEU* 3.5 20.9 - - + -
17H ILE* 1.3 84.3 - - - +
19H ASN* 1.3 69.0 + - - +
20H PHE* 4.0 13.1 - - + -
31H VAL* 3.7 28.3 - - + -
32H TRP 3.6 2.9 - - - +
33H GLY* 4.2 6.1 - - - -
34H SER 4.1 12.8 - - - +
35H ILE* 4.2 17.3 - - + -
45H PHE* 4.2 9.0 - - + -
97H VAL* 4.2 13.5 - - + -
117H LEU* 3.8 20.0 - - + -
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Residues in contact with ASN 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H ALA 3.7 5.8 - - - +
5H VAL* 3.7 18.7 - - - +
17H ILE* 4.3 9.9 - - - +
18H ILE* 1.3 75.8 - - - +
20H PHE* 1.3 65.2 + - - +
30H LYS 3.6 0.2 - - - +
31H VAL* 3.0 9.2 - - - +
32H TRP* 2.7 88.7 + - + +
33H GLY* 4.2 5.5 - - - -
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Residues in contact with PHE 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H LYS* 3.3 6.8 - - - +
4H ALA* 2.8 57.6 + - + +
5H VAL 4.3 0.4 - - - -
6H CYS* 4.3 15.7 - - + -
18H ILE* 4.0 14.8 - - + -
19H ASN* 1.3 76.9 - - - +
21H GLU* 1.3 62.4 + - - +
29H VAL* 4.1 15.9 - - + -
30H LYS 3.2 4.9 - - - -
31H VAL* 3.9 25.4 - - + -
32H TRP* 4.1 3.6 - - - -
84H LEU* 5.0 7.2 - - + -
104H ILE* 4.5 4.3 - - + -
106H LEU* 4.1 7.0 - - + -
112H ILE* 3.6 24.5 - - + -
117H LEU* 4.0 23.1 - - + -
149H ILE* 4.1 25.1 - - + -
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Residues in contact with GLU 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H ALA* 6.2 1.8 - - + -
2H THR 3.8 9.2 - - - +
3H LYS* 3.9 22.1 + - + -
20H PHE* 1.3 78.5 - - - +
22H GLN* 1.3 62.7 + - - +
23H LYS* 3.7 32.6 + - + +
28H PRO 3.9 0.7 - - - +
29H VAL* 3.3 3.0 - - - -
30H LYS* 2.7 53.8 + - + +
32H TRP* 3.7 27.1 - - + -
106H LEU* 4.3 0.4 - - - -
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Residues in contact with GLN 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H ALA* 3.5 0.7 + - - -
2H THR* 3.1 29.5 + - - -
21H GLU* 1.3 75.0 - - - +
23H LYS* 1.3 61.8 + - - +
24H GLU* 3.2 18.8 + - - +
25H SER* 3.4 14.5 + - - -
26H ASN 4.7 0.2 - - - -
27H GLY 3.0 20.8 + - - -
28H PRO 3.7 13.2 - - - +
29H VAL* 3.7 14.3 - - + +
104H ILE 4.6 0.4 + - - -
105H SER* 3.0 22.0 + - - -
106H LEU* 2.7 46.9 + - + +
107H SER* 3.9 3.8 + - - -
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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