Contacts of the strand formed by residues 180 - 185 (chain A) in PDB entry 2QNU
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 ALA 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ALA 4.1 1.4 - - - +
62A ILE* 3.8 0.3 - - - -
63A ALA* 3.0 27.9 + - - +
66A LEU* 3.5 6.5 - - - +
176A ALA 4.0 2.5 - - - +
177A CYS 3.3 13.7 + - - +
178A ASP 3.2 0.8 - - - -
179A GLY* 1.3 80.6 - - - +
181A SER* 1.3 60.2 + - - +
182A HIS* 4.2 5.6 + - + -
197A ARG* 3.7 37.7 - - + +
198A TYR 3.3 13.2 - - - +
200A GLY 3.9 0.4 - - - +
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Residues in contact with SER 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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61A ALA 3.5 4.3 - - - -
62A ILE* 3.8 21.8 - - - -
66A LEU* 4.5 0.2 - - - -
180A ALA* 1.3 73.9 - - - +
182A HIS* 1.3 63.2 + - - +
183A TRP* 3.0 33.4 + - - -
197A ARG* 3.3 5.4 - - - +
198A TYR* 2.9 31.5 + - - +
200A GLY 2.6 25.2 + - - -
201A LEU* 4.6 2.5 - - - -
202A PRO* 3.6 8.0 - - - +
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Residues in contact with HIS 182 (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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60A PHE* 3.1 9.2 - - - +
61A ALA 2.9 35.1 + - - +
105A VAL* 4.3 17.5 - - + -
176A ALA 3.6 24.9 - - - -
177A CYS* 3.8 28.2 + - - +
180A ALA* 4.2 3.0 - - + +
181A SER* 1.3 75.5 - - - +
183A TRP* 1.3 62.3 + - - +
184A TRP* 4.1 3.6 - - + -
195A LEU* 4.0 15.5 - - + -
196A MSE 3.3 2.7 - - - -
197A ARG* 3.7 17.0 - - + +
227A ACT 2.7 41.7 + - - -
172B LEU* 3.7 14.2 - - + +
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Residues in contact with TRP 183 (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 TRP* 4.1 6.3 - + - -
32A TRP* 3.5 28.3 - + - -
58A TRP* 4.2 15.4 - - + -
59A ARG 3.3 6.1 - - - +
60A PHE* 3.5 28.3 - + + -
62A ILE* 4.0 20.9 - - + -
76A VAL* 4.6 8.5 - - + -
181A SER* 3.0 39.7 + - - -
182A HIS* 1.3 77.6 - - - +
184A TRP* 1.3 62.8 + - - +
194A GLY 4.0 0.2 - - - +
195A LEU* 3.4 1.4 - - - +
196A MSE 2.7 63.8 + - + +
198A TYR* 4.0 15.2 - + - -
201A LEU* 5.0 1.3 - - + -
202A PRO* 3.7 26.0 - - + +
210A PHE* 3.7 20.6 - + + -
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Residues in contact with TRP 184 (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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58A TRP* 3.7 13.2 - - - -
59A ARG* 2.8 66.3 + - + +
60A PHE* 3.6 34.8 - - - -
61A ALA* 3.8 4.7 - - + -
104A LEU* 4.6 1.6 - - + -
105A VAL* 4.0 33.2 - - + -
109A ASP* 4.7 0.4 + - - -
112A PHE* 3.7 34.0 - + - -
182A HIS 3.8 5.4 - - - -
183A TRP* 1.3 79.3 - - - +
185A GLY* 1.3 62.9 + - - +
194A GLY 3.3 16.8 - - - +
195A LEU* 3.8 18.2 - - + -
162B ALA 5.6 0.2 - - - +
168B ARG* 3.4 46.9 - - - +
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Residues in contact with GLY 185 (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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57A LEU 4.5 7.0 - - - -
58A TRP* 4.3 4.4 - - - -
59A ARG* 4.3 14.1 - - - -
184A TRP* 1.3 88.6 - - - +
186A ARG* 1.3 64.6 + - - -
187A GLY 3.2 3.7 + - - -
193A ALA* 3.2 22.4 - - - +
194A GLY 3.6 5.5 + - - +
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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