Contacts of the strand formed by residues 333 - 342 (chain A) in PDB entry 1GGE
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 333 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ARG* 5.3 1.6 - - - +
295A PRO* 3.9 0.3 - - - +
296A LEU* 2.9 50.8 + - + +
297A ALA* 4.5 3.8 + - - +
331A PHE* 3.1 19.3 + - + +
332A PRO* 1.3 75.6 - - - +
334A TYR* 1.3 68.9 + - - +
372A LYS* 3.0 30.8 + - + -
373A MET 3.2 6.7 - - - +
374A VAL* 4.1 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A PHE* 3.3 17.4 - + - -
185A PHE* 3.8 27.8 - + - -
266A TYR 2.7 30.3 + - - -
267A ARG* 3.2 15.4 + - - +
269A MET 4.1 9.6 - - - -
293A TRP* 3.6 24.9 - - + -
294A LYS 3.2 6.1 - - - +
295A PRO* 3.8 24.0 - - + -
296A LEU* 4.4 3.4 - - - -
332A PRO* 3.7 28.9 - - + +
333A GLU* 1.3 76.5 - - - +
335A GLU* 1.3 61.3 + - - +
336A LEU 3.9 0.5 + - - -
372A LYS* 3.5 4.1 - - - +
373A MET* 2.9 45.9 + - + +
375A LEU* 4.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 2.6 28.5 + - + +
292A HIS* 3.5 0.5 - - - +
293A TRP* 3.4 4.0 - - - -
294A LYS* 2.7 66.0 + - + +
296A LEU* 4.0 20.0 - - + +
334A TYR* 1.3 72.5 - - - +
336A LEU* 1.3 69.1 + - - +
337A GLY* 3.6 1.1 + - - -
369A ARG* 3.0 41.9 - - + +
371A GLY 3.3 14.1 - - - +
372A LYS* 4.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PHE* 3.7 35.0 - - + -
152A PHE* 4.8 4.5 - - + -
153A LEU* 4.5 5.2 - - + -
189A PHE* 4.8 8.1 - - + -
196A PHE* 6.2 0.9 - - + -
198A LEU* 4.0 26.5 - - + -
291A PHE* 4.8 0.9 - - + -
292A HIS 3.3 17.7 - - - +
293A TRP* 3.6 29.0 - - + -
335A GLU* 1.3 75.5 - - - +
337A GLY* 1.3 61.6 + - - +
338A PHE* 4.0 22.4 - - + -
370A VAL* 2.8 36.1 + - + -
371A GLY 2.9 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PHE* 3.7 0.3 - - - -
292A HIS* 2.8 33.8 + - - +
294A LYS* 6.0 1.3 - - - -
335A GLU* 3.6 2.1 + - - -
336A LEU* 1.3 75.5 - - - +
338A PHE* 1.3 69.5 + - - -
367A VAL* 3.5 20.2 - - - -
368A GLN 3.1 13.0 - - - -
369A ARG* 4.4 0.9 - - - -
370A VAL* 4.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 3.8 20.9 - - + -
147A ILE* 4.5 3.6 - - + -
152A PHE* 6.0 0.2 - + - -
153A LEU* 3.9 22.7 - - + -
279A LEU* 3.7 35.4 - - + -
289A VAL* 3.6 9.2 - - + -
290A ARG 3.5 2.2 - - - -
291A PHE* 3.5 36.3 - + - -
336A LEU* 4.0 17.3 - - + -
337A GLY* 1.3 81.8 - - - -
339A GLN* 1.3 63.4 + - - +
340A LEU* 3.8 16.6 + - + +
366A PRO 3.7 1.0 - - - +
367A VAL* 3.6 1.9 - - - +
368A GLN* 2.8 34.8 + - + +
370A VAL* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A PHE 3.7 0.3 - - - +
289A VAL* 3.2 8.0 - - - +
290A ARG* 2.8 48.7 + - + +
292A HIS* 2.8 30.5 + - - +
338A PHE* 1.3 71.6 - - - +
340A LEU* 1.3 59.7 + - - +
341A ILE* 4.2 2.2 + - - +
360A ILE* 2.8 52.8 + - + +
361A PRO 3.9 2.0 + - - -
362A GLU* 4.1 6.7 - - - +
365A VAL* 3.0 35.3 + - + +
366A PRO 3.8 4.9 - - - +
367A VAL* 3.8 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ILE* 3.7 22.2 - - + -
279A LEU* 3.6 29.6 - - + -
287A THR* 4.0 17.5 - - + -
288A PHE 3.4 0.7 - - - -
289A VAL* 3.7 21.5 - - + -
338A PHE* 3.8 13.3 + - + +
339A GLN* 1.3 73.5 - - - +
341A ILE* 1.3 60.7 + - - +
342A PRO* 4.2 4.4 - - - +
365A VAL* 3.5 17.4 - - - +
366A PRO 4.6 1.6 + - - -
368A GLN* 3.3 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A THR* 6.4 0.4 - - + -
287A THR* 3.8 3.3 - - - +
288A PHE* 2.9 42.3 + - + +
339A GLN 5.1 2.2 - - - +
340A LEU* 1.3 80.4 - - - +
342A PRO* 1.3 82.1 - - + +
345A ASP* 3.6 23.3 - - + +
349A PHE* 3.6 21.3 - - + -
353A LEU* 3.5 42.8 - - + -
360A ILE* 3.9 17.7 - - + -
365A VAL* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A THR* 4.7 8.5 - - + -
288A PHE* 4.1 0.9 - - - -
340A LEU 4.2 4.3 - - - +
341A ILE* 1.3 95.0 - - + +
343A GLU* 1.3 65.6 + - - +
344A GLU* 3.3 29.8 - - + +
345A ASP* 2.9 37.7 + - - +
346A GLU 3.8 1.4 + - - -
----------------------------------------------------------
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