Contacts of the strand formed by residues 368 - 377 (chain D) 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 GLN 368 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D GLY* 3.1 3.0 - - - -
338D PHE* 2.8 38.3 + - + +
340D LEU* 3.5 39.2 + - + +
365D VAL* 6.1 0.8 - - - +
366D PRO* 4.0 16.1 + - + +
367D VAL* 1.3 74.8 - - - +
369D ARG* 1.3 65.4 + - - +
370D VAL* 3.4 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 369 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D TYR* 4.0 23.4 + - + +
142D LYS* 6.0 1.6 - - - +
144D LEU* 5.7 2.3 - - - +
294D LYS* 5.9 2.8 - - - +
335D GLU* 2.9 45.3 + - - +
336D LEU 4.0 4.9 - - - -
337D GLY* 4.4 2.0 - - - -
367D VAL* 4.6 9.2 - - + +
368D GLN* 1.3 73.4 - - - +
370D VAL* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 370 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D PHE* 4.6 0.7 - - + -
140D PRO* 3.3 5.5 - - - +
141D TYR* 2.9 25.5 + - - +
142D LYS* 4.5 2.9 + - - +
144D LEU* 3.5 30.7 - - + +
153D LEU* 3.8 20.9 - - + -
336D LEU* 2.9 23.3 + - + +
338D PHE* 3.5 42.4 - - + +
368D GLN* 3.4 17.9 - - + +
369D ARG* 1.3 75.4 - - - +
371D GLY* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 371 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D PHE* 3.9 13.7 - - - -
139D GLN 3.3 12.6 - - - -
141D TYR* 3.5 16.5 - - - -
335D GLU* 3.3 10.6 - - - +
336D LEU* 2.9 23.0 + - - +
370D VAL* 1.3 83.2 - - - +
372D LYS* 1.3 61.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 372 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D TYR* 3.9 2.5 - - - +
138D PHE* 3.3 6.4 - - - -
139D GLN* 3.0 33.8 + - + +
141D TYR* 3.7 20.4 - - + +
296D LEU* 3.6 24.6 - - + +
333D GLU* 3.4 24.9 + - - -
334D TYR 3.4 9.0 - - - +
371D GLY* 1.3 75.5 - - - -
373D MET* 1.3 72.1 + - - +
374D VAL* 4.1 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D TYR 3.3 11.4 - - - +
138D PHE* 4.3 4.2 - - + +
162D VAL* 3.6 27.1 - - + -
164D VAL* 3.7 22.2 - - + -
185D PHE* 3.8 18.4 - - + -
187D THR* 3.7 15.9 - - - +
189D PHE* 5.1 0.4 - - - -
293D TRP* 3.6 40.1 - - + -
332D PRO 3.8 0.5 - - - +
333D GLU* 3.3 5.0 - - - +
334D TYR* 2.7 47.4 + - + +
372D LYS* 1.3 75.0 - - - +
374D VAL* 1.3 65.2 + - - +
375D LEU* 3.8 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 374 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D GLY* 3.0 3.6 - - - -
137D TYR* 2.9 71.3 + - + +
331D PHE* 3.6 35.4 - - + -
332D PRO 3.6 2.9 - - - -
333D GLU* 3.8 22.0 - - + +
372D LYS* 4.1 19.5 - - + -
373D MET* 1.3 77.9 - - - +
375D LEU* 1.3 62.6 + - - +
376D ASN* 3.7 3.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 375 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D ALA* 4.3 12.3 - - + +
135D HIS 3.5 8.7 - - - +
136D GLY* 4.2 3.1 - - - +
162D VAL* 4.0 8.5 - - + -
164D VAL* 3.7 30.5 - - + -
166D PHE* 3.8 36.3 - - + -
322D LEU* 4.9 0.4 - - + -
326D ILE* 3.6 10.0 - - + +
331D PHE* 3.1 20.0 - - - +
332D PRO* 2.9 33.5 + - + +
334D TYR* 4.0 14.8 - - + -
373D MET* 3.8 15.5 - - + -
374D VAL* 1.3 78.1 - - - +
376D ASN* 1.3 58.3 + - - +
377D ARG 3.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 376 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ALA* 5.2 2.1 - - - +
60D THR* 3.5 28.2 + - + +
61D ARG 5.5 3.4 + - - -
62D ASN* 5.1 4.3 + - - -
65D LEU* 5.3 1.0 - - - +
135D HIS 3.0 3.2 + - - +
136D GLY* 3.7 14.2 - - - -
137D TYR* 3.8 28.0 - - - -
326D ILE* 3.7 8.4 - - - +
331D PHE* 3.5 41.9 - - + -
374D VAL* 4.3 3.4 - - + -
375D LEU* 1.3 74.4 - - - +
377D ARG* 1.3 68.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLY* 3.5 15.0 - - - +
54D SER* 3.5 29.8 - - - +
57D ALA* 3.8 23.1 + - + -
60D THR* 3.8 25.8 - - + -
61D ARG* 3.8 11.7 - - - +
65D LEU* 3.6 40.1 - - + +
72D ARG* 3.7 8.9 - - - +
134D ALA* 3.7 2.5 - - - -
135D HIS* 2.8 37.4 + - + +
326D ILE* 3.6 8.5 - - - +
375D LEU 3.8 0.2 - - - -
376D ASN* 1.3 84.6 - - - +
378D ASN* 1.3 87.2 + - - +
379D PRO* 3.9 5.7 - - - +
380D ASP* 3.5 21.0 + - - +
385D GLU* 4.5 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