Contacts of the strand formed by residues 244 - 250 (chain A) in PDB entry 2QQK
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 ILE 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A THR* 4.2 7.2 - - + -
179A ILE 3.3 7.6 - - - +
180A LEU* 3.4 21.1 - - + -
187A ILE* 4.3 2.5 - - - -
217A ASP* 4.2 2.3 - - - +
218A GLY* 3.7 36.2 + - - -
219A ILE* 4.2 19.7 - - + +
240A SER* 4.0 4.3 + - - -
242A THR* 3.4 22.1 - - + +
243A GLY* 1.3 83.7 - - - +
245A LEU* 1.3 66.1 + - - +
246A SER* 3.8 11.2 - - - +
442A SER* 5.0 6.1 - - - +
444A LEU* 3.3 41.5 - - + +
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Residues in contact with LEU 245 (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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177A PHE 4.1 0.2 - - - +
179A ILE* 2.7 42.6 + - + +
187A ILE* 4.0 26.7 - - + +
189A LEU* 3.4 40.8 - - + -
215A ILE* 4.2 7.6 - - + -
216A TRP 3.6 16.2 - - - +
217A ASP* 4.7 0.2 - - - -
226A ILE* 4.1 22.7 - - + -
238A LEU* 4.6 8.3 - - + -
240A SER* 4.2 21.1 - - - +
244A ILE* 1.3 77.6 - - - +
246A SER* 1.3 61.9 + - - +
247A LEU* 5.0 1.3 - - + -
335A PHE* 4.4 6.5 - - + -
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Residues in contact with SER 246 (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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177A PHE 3.2 5.4 - - - -
178A THR* 2.7 31.9 + - - +
215A ILE* 3.3 2.9 - - - -
216A TRP* 2.7 40.0 + - - -
218A GLY 3.1 20.7 + - - -
219A ILE* 4.4 0.7 - - - +
220A PRO* 3.8 21.1 - - - +
244A ILE* 3.8 2.4 - - - +
245A LEU* 1.3 76.7 + - - +
247A LEU* 1.3 66.6 + - - +
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Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A ILE* 4.4 21.5 - - + -
176A THR* 3.2 7.6 - - - -
177A PHE* 2.7 48.0 + - + +
179A ILE* 6.3 1.8 - - + -
189A LEU* 4.0 19.1 - - + -
191A PHE* 3.9 27.4 - - + -
213A LEU* 4.1 24.2 - - + -
214A ASP 3.3 5.6 - - - +
215A ILE* 3.6 27.6 - - + -
216A TRP* 4.6 0.2 - - - -
220A PRO* 4.8 0.2 - - - +
245A LEU* 5.0 1.6 - - + -
246A SER* 1.3 86.5 - - - +
248A THR* 1.3 62.9 + - - +
249A PHE 4.1 0.7 - - - -
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Residues in contact with THR 248 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A PRO* 5.4 11.1 - - + +
174A ASP* 6.1 0.7 - - - +
175A CYS 3.3 7.9 - - - +
176A THR* 4.4 5.8 - - + +
212A TRP* 3.7 10.0 - - - +
213A LEU* 3.3 6.4 - - - -
214A ASP* 2.8 51.4 + - - +
216A TRP* 3.1 15.7 + - - -
220A PRO* 3.6 16.6 - - - +
221A HIS* 5.2 10.8 - - + +
247A LEU* 1.3 74.0 + - - +
249A PHE* 1.3 64.7 + - - +
250A HIS* 3.9 2.0 + - + -
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Residues in contact with PHE 249 (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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162A SER* 3.8 27.4 - - - -
163A PRO* 5.1 0.7 - - + -
169A TYR* 4.0 27.1 - + + -
173A LEU* 3.1 25.5 - - + +
174A ASP* 3.5 1.9 - - - +
175A CYS* 2.8 37.5 + - + +
177A PHE* 4.1 21.7 - + + -
196A LEU* 3.6 27.8 - - + -
211A ASP* 5.6 0.7 - - + -
212A TRP 3.4 17.3 - - - -
213A LEU* 4.2 9.9 - - + -
247A LEU 4.1 0.6 - - - -
248A THR* 1.3 74.2 - - - +
250A HIS* 1.3 63.6 + - - +
251A THR* 3.3 32.1 - - + -
260A PHE* 4.1 13.9 - + - -
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Residues in contact with HIS 250 (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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172A ASN* 5.9 2.2 - - - -
173A LEU 3.2 2.8 + - - -
174A ASP* 2.8 31.4 + - - +
210A TYR 3.6 21.7 + - - -
211A ASP* 3.2 5.2 - - - +
212A TRP* 2.8 92.7 + + - +
248A THR* 3.9 3.6 + - + -
249A PHE* 1.3 76.5 - - - +
251A THR* 1.3 80.2 + - - +
252A ASP* 5.4 3.0 + - - -
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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