Contacts of the strand formed by residues 162 - 168 (chain A) in PDB entry 3QEL
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 HIS 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A TRP 3.4 0.4 - - - -
161A ASN* 1.3 98.0 + - + +
163A VAL* 1.3 65.2 + - - +
211A LYS* 3.6 9.7 + - + +
213A ASP* 3.1 33.2 + - - +
237A ALA* 3.5 17.8 - - + +
238A ARG 4.6 0.3 + - - -
239A VAL* 3.7 15.8 + - - +
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Residues in contact with VAL 163 (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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155A MET* 3.9 30.5 - - + -
160A TRP* 4.1 9.9 - - + +
162A HIS* 1.3 83.5 - - - +
164A ILE* 1.3 65.4 + - - +
165A LEU* 4.8 0.7 - - + +
180A LEU* 5.2 4.5 - - + -
184A LEU* 5.2 0.4 - - + -
211A LYS 3.4 6.3 + - - +
212A ALA* 3.4 21.1 - - + +
213A ASP* 2.8 31.6 + - - +
214A LYS 3.9 0.5 + - - -
237A ALA* 4.1 2.8 - - - +
239A VAL* 3.4 26.5 - - + +
241A ILE* 3.7 25.1 - - + -
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Residues in contact with ILE 164 (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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163A VAL* 1.3 76.8 - - - +
165A LEU* 1.3 69.9 + - - +
166A ILE* 4.2 13.5 - - + -
213A ASP* 5.0 4.7 - - + -
214A LYS* 3.5 14.4 - - + +
216A LEU* 4.4 8.3 - - + -
232A ALA* 3.3 45.3 - - + +
235A LEU* 4.3 11.4 - - + -
237A ALA* 3.2 33.7 - - + +
239A VAL 2.8 9.7 + - - +
240A ILE* 3.4 14.8 - - + +
241A ILE* 2.9 26.7 + - - +
266A TYR* 6.5 0.4 - - + -
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Residues in contact with LEU 165 (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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151A TRP* 4.8 5.4 - - + -
163A VAL* 4.1 2.1 - - + -
164A ILE* 1.3 75.2 - - - +
166A ILE* 1.3 67.1 + - - +
167A VAL* 3.6 22.9 - - + -
176A ALA 4.9 0.9 - - - +
177A GLN* 3.9 40.6 - - + +
180A LEU* 4.0 23.3 - - + -
181A GLU* 5.3 2.9 - - + -
212A ALA* 5.3 6.5 - - + +
214A LYS 3.0 7.9 + - - +
215A VAL* 3.2 20.2 - - + +
216A LEU* 2.8 27.5 + - - +
241A ILE* 3.6 33.0 - - + +
242A LEU* 5.2 0.4 - - - -
243A SER 5.2 0.7 - - - +
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Residues in contact with ILE 166 (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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164A ILE* 4.2 10.8 - - + -
165A LEU* 1.3 77.2 - - - +
167A VAL* 1.3 63.3 + - - +
216A LEU* 3.4 13.2 - - + +
218A PHE* 4.0 16.2 - - + -
228A LEU* 3.9 24.7 - - + -
229A LEU* 4.2 24.5 - - + -
232A ALA* 5.1 4.9 - - + -
240A ILE* 3.4 31.4 - - + -
241A ILE 2.8 13.2 + - - +
242A LEU* 3.3 17.7 - - + +
243A SER 3.0 24.1 + - - -
252A VAL* 5.0 7.0 - - + -
268A TRP* 4.9 4.9 - - + -
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Residues in contact with VAL 167 (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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165A LEU* 3.6 31.2 - - + -
166A ILE* 1.3 79.5 - - - +
168A SER* 1.3 67.1 + - - +
169A ASP* 5.6 0.2 - - - -
173A GLY* 3.5 29.6 - - - +
174A ARG* 4.6 2.7 - - + +
176A ALA* 4.8 0.2 - - + -
177A GLN* 4.0 24.2 - - + +
215A VAL* 4.5 3.6 - - + -
216A LEU 3.0 13.6 + - - +
217A GLN* 3.2 15.7 - - + -
218A PHE* 3.2 28.3 + - - -
243A SER* 3.4 14.8 - - - +
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Residues in contact with SER 168 (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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167A VAL* 1.3 76.9 - - - +
169A ASP* 1.3 58.1 + - - +
170A ASP* 2.5 42.6 + - - -
173A GLY* 3.1 23.6 + - - -
174A ARG 3.8 0.7 + - - -
218A PHE* 3.6 31.3 - - - -
220A PRO* 4.4 6.1 - - - -
243A SER 3.0 13.0 + - - -
244A ALA* 4.2 10.7 - - - -
245A SER 4.9 1.3 + - - -
248A ASP* 5.1 2.7 - - - -
273A ARG* 5.2 1.7 + - - -
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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