Contacts of the strand formed by residues 260 - 264 (chain A) in PDB entry 5H15
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 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A MET* 4.4 6.3 - - + -
253A SER 3.2 6.7 - - - +
254A CYS* 3.6 22.2 - - + -
258A HIS 5.0 2.2 - - - +
259A SER* 1.3 76.2 - - - +
261A LYS* 1.3 61.2 + - - +
299A PHE* 4.6 1.7 - - - -
300A SER* 3.5 3.1 - - - -
301A THR* 3.0 35.0 + - + +
302A ARG* 6.3 0.2 - - - -
304A ILE* 3.8 21.5 - - + -
305A HIS* 4.0 10.3 - - + -
309A VAL* 4.0 3.8 - - + -
312A VAL* 3.7 25.1 - - + -
321A SER* 3.7 23.8 - - - +
331A TRP* 3.6 33.4 - - + -
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Residues in contact with LYS 261 (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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233A GLU 3.6 19.1 + - - +
234A GLY 3.5 26.3 + - - -
235A HIS* 3.7 21.7 + - + +
236A ARG* 6.1 0.6 - - - +
252A MET* 3.5 6.3 - - - -
253A SER* 2.8 48.1 + - - +
257A ASP* 4.2 2.0 + - - -
259A SER* 3.4 20.5 + - - +
260A LEU* 1.3 74.0 - - - +
262A LEU* 1.4 58.5 + - - +
263A TRP* 3.5 16.9 - - + +
297A PRO* 4.0 6.3 - - + -
299A PHE 3.4 6.1 - - - +
300A SER* 2.7 37.4 + - - +
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Residues in contact with LEU 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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250A LYS* 4.0 12.3 - - + -
251A ILE 3.5 8.1 - - - +
252A MET* 3.8 13.3 - - + -
261A LYS* 1.4 70.4 - - - +
263A TRP* 1.3 60.7 + - - +
264A ARG* 3.7 35.9 - - + +
297A PRO* 3.2 7.3 - - - +
298A ASP* 2.7 42.0 + - + +
299A PHE* 2.9 32.4 + - + +
314A TRP* 3.5 38.8 - - + -
333A PRO* 5.7 0.4 - - + -
340A ILE* 4.8 7.6 - - + -
343A ILE* 4.7 4.0 - - + -
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Residues in contact with TRP 263 (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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215A LEU* 3.8 14.2 - - + +
229A PHE* 3.5 45.1 - + + -
230A GLY 4.0 9.9 - - - -
234A GLY* 4.0 23.6 - - - -
235A HIS* 4.7 2.7 - + - -
250A LYS* 3.4 1.9 - - - -
251A ILE* 2.8 58.2 + - + +
253A SER* 2.8 26.8 + - - -
261A LYS* 3.5 36.2 + - + +
262A LEU* 1.3 73.6 - - - +
264A ARG* 1.3 62.5 + - - +
265A ILE* 3.7 2.5 + - - +
294A ILE* 3.7 26.2 - - + -
295A HIS 4.9 0.2 - - - -
296A PHE 3.8 4.0 - - - -
297A PRO* 3.6 32.3 - - + -
298A ASP* 4.0 3.4 - - - -
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Residues in contact with ARG 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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229A PHE* 5.2 1.4 - - - -
249A GLU 3.9 3.6 - - - -
250A LYS* 4.1 16.5 - - + +
262A LEU* 3.7 21.1 - - + +
263A TRP* 1.3 72.0 - - - +
265A ILE* 1.3 64.0 + - - +
266A ASN* 3.6 19.6 - - - +
267A SER* 3.9 14.9 + - - +
270A MET* 3.8 12.1 - - - +
298A ASP* 3.1 40.8 + - + +
340A ILE 2.8 23.6 + - - -
341A ASP* 3.1 36.0 + - - +
343A ILE* 3.5 23.8 + - - +
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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