Contacts of the strand formed by residues 246 - 252 (chain A) in PDB entry 4NKQ
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 GLN 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A ARG* 4.9 0.4 - - - +
179A GLN* 5.5 1.0 + - - -
203A MET* 3.4 34.0 - - + +
204A PRO* 3.7 16.8 + - - +
205A SER* 4.0 14.3 + - - -
206A SER* 4.3 0.4 + - - -
241A ASP 5.8 1.6 + - - -
242A GLU* 5.7 4.2 + - - +
244A GLN 4.0 8.4 + - - +
245A PRO* 1.3 77.6 - - - +
247A ASN* 1.3 67.5 + - + +
248A LEU* 3.5 2.4 - - - +
262A TRP* 3.5 2.1 - - - +
263A GLU* 2.5 52.2 + - + +
264A VAL* 5.7 0.2 - - - -
265A ARG* 6.3 0.2 - - - -
301A HIS* 2.8 36.6 + - + -
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Residues in contact with ASN 247 (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 ARG* 3.8 13.6 - - - +
203A MET* 3.8 22.2 - - - +
246A GLN* 1.3 79.7 - - - +
248A LEU* 1.3 66.3 + - - +
249A GLU* 3.3 30.5 + - - +
261A SER* 3.6 7.3 + - - +
262A TRP* 3.9 2.9 - - - -
263A GLU* 2.5 31.4 + - - +
303A ARG* 4.4 9.3 - - - +
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Residues in contact with LEU 248 (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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246A GLN 3.5 2.6 - - - +
247A ASN* 1.3 75.8 - - - +
249A GLU* 1.3 63.4 + - - +
250A CYS* 4.8 6.1 - - - -
261A SER 3.2 21.1 - - - +
262A TRP* 3.6 19.3 - - + +
276A LEU* 4.3 7.6 - - + -
321A VAL* 3.8 32.8 - - + +
322A SER* 4.9 0.2 - - - -
323A VAL* 4.0 25.6 - - + +
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Residues in contact with GLU 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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247A ASN* 3.4 30.6 + - - +
248A LEU* 1.3 80.1 - - - +
250A CYS* 1.3 64.9 + - - +
251A PHE* 4.1 26.9 - - + -
259A SER 4.0 0.7 - - - +
260A CYS* 3.2 3.3 - - - -
261A SER* 2.8 45.2 + - - +
303A ARG* 4.7 8.5 + - - -
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Residues in contact with CYS 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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248A LEU* 4.8 6.3 - - - -
249A GLU* 1.3 79.1 - - - +
251A PHE* 1.3 74.3 + - - +
258A LEU* 3.7 12.7 - - + +
259A SER 3.6 4.3 - - - -
260A CYS* 2.0 45.5 - - - -
321A VAL* 3.9 25.4 - - + -
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Residues in contact with PHE 251 (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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249A GLU* 4.1 35.2 - - + -
250A CYS* 1.3 84.1 - - - +
252A PHE* 1.3 63.1 + - - +
253A ASP 4.2 0.2 + - - -
257A VAL 3.8 0.5 - - - +
258A LEU* 3.2 6.9 - - - +
259A SER* 2.9 39.7 + - - +
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Residues in contact with PHE 252 (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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251A PHE* 1.3 77.3 - - - +
253A ASP* 1.3 78.2 + - - +
254A GLY* 3.2 32.0 + - - -
255A ALA 3.0 23.3 - - - -
256A ALA* 3.5 2.7 - - - -
257A VAL 3.2 26.0 - - - -
258A LEU* 3.9 14.8 - - + +
310A VAL* 3.7 17.9 - - + -
313A PRO* 4.0 21.1 - - + -
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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