Contacts of the strand formed by residues 176 - 181 (chain A) in PDB entry 1ATK
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 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A VAL* 4.0 2.6 - - - +
170A GLY 3.3 6.5 - - - -
171A ILE* 4.0 19.5 - - + +
174A GLY 3.9 1.9 + - - +
175A ASN* 1.3 74.0 - - - +
177A HIS* 1.3 60.7 + - - +
197A ALA* 3.8 4.5 - - - +
198A ARG* 2.9 58.8 + - - +
199A ASN* 3.8 26.8 - - + +
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Residues in contact with HIS 177 (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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149A VAL* 3.7 17.0 - - + +
169A TYR* 3.3 0.7 - - - -
170A GLY* 2.9 34.8 + - - -
171A ILE 3.5 22.4 + - - -
172A GLN* 3.7 26.0 + - + +
175A ASN 3.7 11.7 + - - -
176A LYS* 1.3 76.4 - - - +
178A TRP* 1.3 67.6 + - - +
179A ILE* 3.8 13.9 - - + +
195A LEU* 3.3 35.5 - - + +
196A MET 3.0 13.9 - - - +
198A ARG* 3.1 16.7 + - - +
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Residues in contact with TRP 178 (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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118A GLU* 2.9 36.5 + - + -
121A LEU* 3.5 31.0 - - + -
122A LYS* 3.5 27.8 - - + -
125A VAL* 4.1 12.1 - - + -
166A ALA* 4.9 5.4 - - + -
168A GLY 3.5 19.5 - - - +
169A TYR* 3.7 26.5 - + + -
177A HIS* 1.3 76.1 - - - +
179A ILE* 1.3 59.2 + - - +
180A ILE* 3.5 19.8 + - + +
194A ILE 3.5 1.4 - - - +
195A LEU* 3.3 7.3 - - - -
196A MET* 2.7 32.6 + - + +
197A ALA 3.8 17.7 - - - -
198A ARG* 3.5 24.4 - - + +
206A ILE* 3.8 23.5 - - + +
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Residues in contact with ILE 179 (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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5A VAL 3.9 6.3 - - - +
6A ASP* 3.9 27.4 - - + +
8A ARG* 3.4 32.1 - - - +
165A LEU 3.6 0.2 - - - +
166A ALA* 3.7 2.8 - - - -
167A VAL* 2.7 43.9 + - + +
168A GLY* 3.0 18.0 + - - +
169A TYR* 3.9 17.9 - - - +
177A HIS* 3.8 24.0 - - + +
178A TRP* 1.3 70.8 - - - +
180A ILE* 1.3 56.7 + - - +
193A TYR* 4.1 8.1 - - + -
194A ILE 3.9 2.9 - - - +
195A LEU* 4.1 9.9 - - + -
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Residues in contact with ILE 180 (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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133A VAL* 4.2 4.3 - - + -
135A ILE* 5.1 1.1 - - + -
164A VAL* 3.4 35.4 - - + -
165A LEU 3.3 1.8 - - - +
166A ALA* 3.7 28.3 - - + +
178A TRP* 4.1 12.8 - - + -
179A ILE* 1.3 74.5 - - - +
181A LYS* 1.3 61.4 + - - +
193A TYR* 3.3 7.9 - - - -
194A ILE* 2.8 58.8 + - + +
196A MET* 3.8 26.7 - - + -
206A ILE* 3.8 22.7 - - + -
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Residues in contact with LYS 181 (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 VAL* 3.7 20.6 - - + +
14A THR* 2.6 45.1 + - - +
15A PRO 3.3 11.8 + - - -
16A VAL* 3.7 17.9 - - + +
17A LYS* 4.7 6.3 - - - +
32A GLY* 5.7 2.2 - - - -
35A GLU* 4.9 2.6 + - - -
164A VAL* 3.0 17.8 - - - +
165A LEU* 2.8 42.7 + - + +
167A VAL* 4.6 4.7 - - + -
179A ILE 4.1 0.8 + - - -
180A ILE* 1.3 70.5 - - - +
182A ASN* 1.3 70.7 + - - +
192A GLY 4.0 0.2 - - - -
193A TYR* 3.5 27.9 - - + +
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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