Contacts of the strand formed by residues 311 - 316 (chain A) in PDB entry 1E2R
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 GLU 311 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ALA* 3.9 2.3 - - - +
306A SER* 3.0 32.7 + - - +
309A ARG* 2.7 61.7 + - + +
310A PRO* 1.3 78.6 - - - +
312A PHE* 1.3 64.9 + - - +
324A LEU* 3.6 30.5 - - + +
325A VAL 3.0 8.7 - - - +
326A ASP* 3.7 26.7 - - + +
327A TYR* 3.4 12.8 - - - -
336A THR* 4.9 2.3 + - - -
371A THR* 4.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 4.8 0.4 - - + -
247A THR 3.5 27.4 - - - -
248A SER* 3.6 20.0 - - - -
257A TYR* 4.0 26.0 - - + -
258A ALA 4.3 0.2 - - - -
259A ILE* 3.5 55.6 - - + -
270A ILE* 4.3 17.7 - - + -
303A ILE* 4.6 0.4 - - + -
304A LEU 3.6 11.2 - - - +
305A ALA* 4.1 6.5 - - + -
311A GLU* 1.3 75.6 - - - +
313A ILE* 1.3 62.7 + - - +
314A VAL* 3.9 5.6 - - + -
323A LEU 3.3 3.3 - - - +
324A LEU* 3.3 4.0 - - - -
325A VAL* 2.9 35.2 + - + +
327A TYR* 3.4 26.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ALA 3.9 1.0 - - - +
303A ILE* 3.1 6.1 - - - -
304A LEU* 2.8 48.0 + - + +
305A ALA 4.1 4.3 - - - -
306A SER* 3.9 26.9 - - - +
312A PHE* 1.3 75.0 - - - +
314A VAL* 1.3 61.1 + - - +
315A ASN 4.2 0.2 - - - -
322A ILE* 4.0 12.1 - - + -
323A LEU 3.4 2.9 - - - -
324A LEU* 3.8 17.0 - - + -
349A LEU* 4.2 14.1 - - + -
356A PHE* 3.5 39.6 - - + -
369A ILE* 6.2 0.2 - - + -
371A THR* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ILE* 4.0 26.9 - - + -
268A TYR* 4.3 17.5 - - + -
300A VAL* 3.7 29.8 - - + -
302A ALA 4.0 1.6 - - - -
303A ILE* 4.2 8.5 - - + -
312A PHE* 4.5 0.7 - - + -
313A ILE* 1.3 80.1 - - - +
315A ASN* 1.3 69.9 + - - +
316A VAL* 3.7 6.7 + - + -
321A LYS 3.8 0.3 - - - +
322A ILE* 3.4 3.8 - - - -
323A LEU* 2.8 51.0 + - + +
325A VAL* 4.2 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A VAL* 3.5 8.5 - - - +
301A ALA* 2.9 29.3 + - + -
302A ALA* 3.0 28.7 + - - +
313A ILE 4.1 0.2 + - - -
314A VAL* 1.3 70.9 - - - +
316A VAL* 1.3 60.5 + - - +
317A LYS 3.8 0.4 - - - -
321A LYS 4.0 2.0 - - - -
322A ILE* 3.4 17.5 - - - +
344A LEU* 3.9 14.7 - - + +
345A HIS 3.1 19.4 + - - -
356A PHE* 3.3 29.4 - - - -
358A THR* 2.9 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A THR* 4.0 21.5 - - + +
298A PRO* 3.4 31.9 - - + +
299A ARG 3.7 2.7 - - - +
300A VAL* 5.0 0.7 - - + -
314A VAL* 4.2 3.6 - - + +
315A ASN* 1.3 75.4 - - - +
317A LYS* 1.3 64.6 + - - +
319A THR* 3.1 21.8 - - - +
320A GLY* 3.1 18.2 + - - -
321A LYS* 2.8 26.4 + - + +
323A LEU* 3.9 33.7 - - + -
344A LEU* 3.6 3.8 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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