Contacts of the strand formed by residues 244 - 249 (chain A) in PDB entry 3JRQ
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 SER 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A VAL 3.5 7.0 - - - -
176A TYR* 3.5 22.6 - - - -
188A CYS* 5.2 0.2 - - - -
192A MET* 3.6 6.3 - - - +
225A PHE* 3.2 32.4 - - - -
243A THR* 1.3 81.9 - - - +
245A VAL* 1.3 59.4 + - - +
246A VAL* 4.0 0.7 - - - +
258A ASN* 3.6 0.8 - - - -
259A CYS 2.8 33.3 + - - -
262A SER* 5.1 0.2 - - - -
315A ILE* 3.9 17.3 - - - -
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Residues in contact with VAL 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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174A GLY* 3.3 2.6 - - - -
175A VAL* 2.9 51.1 + - + -
244A SER* 1.3 74.2 + - - +
246A VAL* 1.3 62.8 + - - +
256A VAL* 4.1 8.3 - - + -
257A ALA 3.5 7.0 - - - +
258A ASN* 3.6 20.9 - - + +
262A SER* 3.6 22.6 - - - -
263A ARG 4.3 4.7 - - - +
264A ALA* 3.9 33.2 - - + +
344A LEU* 3.6 19.1 - - + +
345A ALA 4.8 0.9 - - - +
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Residues in contact with VAL 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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172A PHE* 3.5 43.7 - - + -
173A PHE 3.2 4.7 - - - +
174A GLY* 4.3 0.4 - - - -
176A TYR* 3.9 7.9 - - + +
192A MET* 3.9 13.7 - - + -
221A LEU* 4.0 21.3 - - + -
225A PHE* 3.9 24.9 - - + -
244A SER* 4.0 4.7 - - - +
245A VAL* 1.3 77.5 - - - +
247A ALA* 1.3 65.1 + - - +
248A VAL* 4.3 1.3 - - + -
255A PHE 3.9 0.2 - - - +
256A VAL* 3.3 7.7 - - - +
257A ALA* 2.9 32.3 + - + +
344A LEU* 4.4 1.8 - - - -
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Residues in contact with ALA 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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171A HIS 3.7 1.7 - - - +
172A PHE* 3.7 1.2 - - - -
173A PHE* 2.7 42.3 + - + +
246A VAL* 1.3 75.9 - - - +
248A VAL* 1.3 61.8 + - - +
249A VAL* 4.1 3.8 - - + -
254A ILE* 4.7 0.2 - - + -
255A PHE 3.2 9.9 - - - +
256A VAL* 4.4 4.7 - - + -
342A LEU* 3.7 30.3 - - + -
344A LEU* 4.1 16.5 - - + +
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Residues in contact with VAL 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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151A PHE* 4.2 3.8 - - + -
170A ALA* 3.9 14.8 - - + -
171A HIS 3.3 8.5 - - - +
172A PHE* 4.5 6.1 - - + -
196A LEU* 3.8 28.9 - - + -
217A TRP* 3.9 13.5 - - + -
221A LEU* 4.2 17.0 - - + -
246A VAL* 4.3 4.0 - - + -
247A ALA* 1.3 76.9 - - - +
249A VAL* 1.3 62.5 + - - +
250A PHE* 3.4 26.9 + - + -
253A HIS 4.0 0.7 - - - +
254A ILE* 3.4 3.6 - - - -
255A PHE* 2.8 41.5 + - + +
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Residues in contact with VAL 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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169A ALA 4.0 0.5 - - - +
170A ALA* 3.5 2.6 - - - -
171A HIS* 2.9 47.9 + - + +
173A PHE* 3.9 25.4 - - + -
247A ALA* 4.7 1.1 - - + -
248A VAL* 1.3 77.4 - - - +
250A PHE* 1.3 64.1 + - - +
253A HIS 3.9 2.2 - - - -
254A ILE* 4.4 11.4 - - + +
335A ARG* 3.7 25.6 - - - +
342A LEU* 4.1 25.6 - - + -
420A VAL* 4.8 7.6 - - + -
422A LEU* 4.6 10.8 - - + -
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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