Contacts of the strand formed by residues 261 - 269 (chain A) in PDB entry 1R37
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 LEU 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A LYS 4.6 0.7 - - - +
240A GLY* 4.5 1.2 - - - -
241A VAL* 3.5 11.9 - - + +
243A ALA 4.7 0.2 - - - -
244A VAL* 3.7 26.5 - - + +
257A TYR 4.4 0.9 - - - +
258A PRO* 3.2 26.4 + - + +
259A LYS 3.3 3.8 - - - +
260A ALA* 1.3 80.4 - - - +
262A ALA* 1.3 68.0 + - - +
265A GLY* 4.0 18.2 - - - +
266A LYS 4.1 9.2 - - - +
267A TYR* 4.0 24.0 - - + -
289A ILE* 3.9 36.3 - - + +
290A GLN 4.8 0.9 - - - +
291A PHE* 4.9 1.6 - - + -
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Residues in contact with ALA 262 (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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239A LYS* 3.1 29.4 - - + +
240A GLY 3.9 7.6 - - - +
241A VAL 2.8 21.7 + - - +
242A ASP* 4.2 9.9 - - - +
260A ALA 3.7 0.8 + - - -
261A LEU* 1.3 77.4 - - - +
263A LYS* 1.3 70.4 + - - +
264A GLN 3.4 0.2 + - - -
265A GLY* 3.0 12.0 + - - -
287A SER* 5.5 0.9 - - - -
289A ILE* 3.7 8.2 - - - +
103B TYR* 3.6 13.7 - - - +
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Residues in contact with LYS 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ASP* 4.8 3.5 - - - +
262A ALA* 1.3 77.8 - - - +
264A GLN* 1.3 66.2 + - - +
265A GLY 3.2 2.3 + - - -
286A LEU 5.4 1.6 - - - +
287A SER* 3.4 27.1 - - - +
103B TYR* 2.9 41.2 + - + +
111B LEU* 2.7 46.6 + - + +
112B CYS 3.5 10.7 + - - -
113B ASP* 2.9 25.5 + - - +
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Residues in contact with GLN 264 (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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242A ASP 4.3 1.3 - - - +
263A LYS* 1.3 71.8 - - - +
265A GLY* 1.3 65.9 + - - +
266A LYS* 3.4 24.6 + - - +
287A SER 2.8 13.7 + - - -
288A GLU* 3.4 32.1 + - + +
290A GLN* 4.9 1.9 + - - +
102B TYR* 5.6 0.2 - - - -
103B TYR* 3.9 11.9 - - + -
106B ILE* 3.9 9.4 - - - +
108B GLU* 3.4 41.0 + - - +
111B LEU* 3.3 24.9 - - + +
161B ARG* 3.6 4.4 - - - +
165B LYS* 5.0 3.0 - - - +
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Residues in contact with GLY 265 (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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241A VAL 4.3 1.3 - - - -
242A ASP* 3.2 18.8 - - - -
261A LEU* 4.0 13.0 - - - +
262A ALA 3.0 18.0 + - - -
263A LYS 3.1 2.5 + - - -
264A GLN* 1.3 79.2 - - - +
266A LYS* 1.3 60.6 + - - +
289A ILE* 3.3 7.8 - - - +
290A GLN 3.0 25.1 + - - +
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Residues in contact with LYS 266 (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 LYS 3.5 24.0 - - - +
166A ALA* 4.0 15.5 - - - +
167A SER* 3.5 23.8 - - - +
172A LYS* 4.4 11.3 - - - +
242A ASP 3.0 12.9 + - - +
243A ALA* 3.2 3.7 - - - +
244A VAL 2.8 28.4 + - - +
261A LEU* 4.1 1.8 - - - +
264A GLN* 3.4 19.7 + - - +
265A GLY* 1.3 74.6 - - - +
267A TYR* 1.3 61.8 + - - +
268A VAL* 3.6 5.1 + - + +
290A GLN* 3.8 37.1 - - + +
292A VAL* 5.2 5.4 - - + -
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Residues in contact with TYR 267 (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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244A VAL* 3.6 33.3 - - + +
246A ASP* 2.6 40.2 + - + +
249A ASN* 3.9 3.1 - - - -
253A THR 3.8 7.8 + - - -
254A LEU* 3.8 17.3 - - + +
257A TYR* 3.6 17.6 - - + +
258A PRO* 3.6 39.4 - - + +
261A LEU* 4.0 8.5 - - + -
265A GLY 4.0 0.6 + - - -
266A LYS* 1.3 69.4 - - - +
268A VAL* 1.3 64.4 + - - +
269A MET* 3.5 14.6 + - + +
290A GLN 2.8 17.1 + - - +
291A PHE* 3.5 20.7 - + + -
292A VAL* 2.9 25.3 + - - +
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Residues in contact with VAL 268 (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 ALA* 3.9 32.5 - - + +
165A LYS* 4.5 2.5 - - + +
166A ALA* 4.1 22.9 - - + +
244A VAL 2.7 19.0 + - - +
245A ILE* 3.6 7.9 - - + -
246A ASP* 3.0 28.1 + - - +
266A LYS* 4.2 6.7 - - + +
267A TYR* 1.3 71.6 - - - +
269A MET* 1.3 62.3 + - - +
270A VAL* 3.6 4.3 + - + +
292A VAL* 3.3 20.9 - - + +
294A SER* 3.9 27.1 - - - -
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Residues in contact with MET 269 (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 ASN* 3.3 27.1 - - - +
254A LEU* 4.1 11.2 - - + -
267A TYR* 3.7 24.9 - - + +
268A VAL* 1.3 69.2 - - - +
270A VAL* 1.3 59.4 + - - +
277A LEU* 4.3 5.2 - - + -
291A PHE* 4.1 31.4 - - - -
292A VAL 2.8 13.4 + - - +
293A GLY* 3.7 3.1 - - - -
294A SER 3.3 17.9 + - - -
281B ALA* 3.5 37.5 - - + +
284B ILE* 4.1 23.8 - - + -
285B THR* 2.9 22.6 + - - +
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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