Contacts of the strand formed by residues 169 - 173 (chain A) in PDB entry 4QNW
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 GLY 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PHE* 3.2 22.4 - - - -
105A CYS 3.0 18.7 + - - -
163A ILE* 4.2 3.4 - - - -
167A PHE* 3.1 9.6 + - - +
168A ASP* 1.3 81.2 - - - +
170A VAL* 1.3 66.4 + - - +
221A ARG* 3.2 17.5 - - - -
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Residues in contact with VAL 170 (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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104A PHE* 3.4 6.0 - - - -
105A CYS 3.1 13.2 - - - +
107A LEU* 4.0 14.1 - - + -
159A ALA* 4.0 17.0 - - + -
162A ALA* 3.5 29.8 - - + -
163A ILE* 4.0 6.1 - - + -
169A GLY* 1.3 79.5 - - - +
171A GLU* 1.3 60.9 + - - +
172A ILE* 5.0 1.1 - - + -
213A VAL* 3.7 30.3 - - + -
217A VAL* 4.5 2.5 - - + -
221A ARG 2.9 15.1 + - - +
222A VAL* 3.4 3.7 - - + -
223A GLY 2.8 24.1 + - - +
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Residues in contact with GLU 171 (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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29A PRO* 3.6 8.1 - - - +
61A ILE* 3.4 13.1 - - + +
104A PHE* 4.1 1.5 - - + -
105A CYS 2.9 8.1 + - - +
106A GLN* 2.9 38.4 + - + +
107A LEU* 2.8 30.5 + - - +
170A VAL* 1.3 73.8 - - - +
172A ILE* 1.3 73.1 + - - +
173A HIS 3.5 0.3 + - - -
223A GLY 3.3 9.9 - - - +
225A LYS* 3.6 13.4 - - + +
259A TYR* 2.5 32.8 + - - +
261A HIS* 2.8 32.0 + - - -
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Residues in contact with ILE 172 (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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107A LEU* 4.0 6.3 - - + -
155A PHE* 4.7 5.8 - - + -
170A VAL* 5.0 2.7 - - + -
171A GLU* 1.3 75.3 - - - +
173A HIS* 1.3 58.1 + - - +
174A GLY* 2.9 9.7 + - - +
180A ILE* 3.3 31.2 - - + -
206A ALA* 6.5 0.2 - - - -
209A VAL* 4.1 9.4 - - + +
210A THR* 3.7 41.3 - - - +
213A VAL* 4.0 24.5 - - + -
222A VAL* 3.7 23.6 - - + -
223A GLY 2.9 13.8 + - - +
224A VAL* 3.8 9.4 - - + +
225A LYS* 3.0 21.3 + - - +
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Residues in contact with HIS 173 (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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106A GLN* 3.2 34.9 + - - +
107A LEU 3.0 22.0 + - - +
108A TRP* 3.5 35.6 - + + +
109A ALA 5.6 0.5 + - - +
171A GLU 3.5 0.8 + - - -
172A ILE* 1.3 69.8 - - - +
174A GLY* 1.3 57.8 + - - +
175A ALA* 3.1 34.2 + - + +
176A ASN* 3.4 21.0 + - - -
178A TYR* 3.5 21.1 - + + +
179A LEU 5.5 0.3 + - - -
180A ILE* 3.6 19.4 + - - +
225A LYS* 4.6 2.6 - - + +
401A FMN 3.2 19.4 + - - -
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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