Contacts of the strand formed by residues 488 - 495 (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 ARG 488 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ASN* 5.6 0.7 + - - -
486A GLN 3.5 0.4 + - - -
487A GLU* 1.3 85.0 - - - +
489A VAL* 1.3 61.6 + - - +
490A GLU* 2.5 44.5 + - + +
490B GLU* 3.9 25.7 + - - +
491B GLY* 3.4 19.0 - - - +
492B ASN* 3.3 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ASN* 5.3 0.7 - - - +
487A GLU* 3.9 2.2 - - + +
488A ARG* 1.3 77.0 + - - +
490A GLU* 1.3 66.6 + - - +
489B VAL* 4.0 4.3 - - + +
490B GLU* 3.2 2.9 - - - -
491B GLY 2.7 42.2 + - - +
493B LYS* 3.8 39.3 - - + +
97C ALA* 3.8 20.6 - - + -
97D ALA* 3.5 38.4 - - + +
102D PRO* 4.0 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ARG* 2.5 44.2 + - + +
489A VAL* 1.3 83.1 - - - +
491A GLY* 1.3 59.1 + - - +
488B ARG* 4.2 13.7 + - - +
489B VAL 3.2 3.8 - - - -
490B GLU* 4.0 19.7 - - + -
97D ALA 4.5 3.6 + - - +
98D GLY* 4.3 5.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A GLU* 1.3 75.4 - - - +
492A ASN* 1.3 59.3 + - - -
488B ARG* 3.5 20.2 - - - -
489B VAL* 2.7 44.0 + - - +
97D ALA 4.5 1.4 + - - -
98D GLY* 3.6 17.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A GLY* 1.3 74.1 - - - -
493A LYS* 1.3 60.8 + - - +
494A VAL* 3.0 20.1 + - + +
486B GLN* 3.0 37.2 + - + +
487B GLU 3.2 4.7 - - - -
488B ARG* 2.8 47.8 + - - +
97D ALA* 4.6 1.1 - - - -
98D GLY* 3.0 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ASN* 1.3 68.9 - - - +
494A VAL* 1.3 62.0 + - - +
278B ARG* 4.8 2.4 - - - +
402B PHE 5.7 0.2 + - - -
403B THR* 4.8 3.6 - - - +
404B ASN* 2.8 24.6 + - - -
409B GLN* 4.5 0.8 - - - +
484B SER* 4.4 5.9 - - - +
485B TYR 3.7 16.6 - - - +
486B GLN* 3.6 18.5 - - - +
487B GLU* 2.9 46.0 + - + +
489B VAL* 3.8 20.2 - - + -
102C PRO* 4.1 2.7 - - - -
95D LEU* 3.8 17.5 - - + +
96D ARG 3.5 7.2 - - - -
97D ALA* 4.8 0.2 - - - +
104D LEU* 3.8 19.1 - - + -
106D GLU* 2.8 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ASN* 3.5 21.3 - - + +
493A LYS* 1.3 79.1 - - - +
495A ARG* 1.3 59.3 + - - +
496A GLU* 3.5 31.9 + - + +
486B GLN* 3.9 22.2 - - - +
94D SER 3.5 1.6 - - - +
95D LEU* 3.7 6.2 - - - +
96D ARG* 2.8 31.9 + - - +
98D GLY* 3.7 25.6 - - - +
99D SER* 3.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A HIS* 6.3 0.6 - - - -
494A VAL* 1.3 69.9 - - - +
496A GLU* 1.3 59.7 + - - +
482B PHE* 4.3 14.0 + - - -
483B GLU* 4.7 4.1 - - + +
484B SER* 2.8 41.6 + - - +
90D ASP* 2.8 48.7 - - + +
93D ASN* 3.7 16.2 + - - +
94D SER 3.4 6.7 - - - +
95D LEU* 3.7 26.3 - - + +
106D GLU 4.9 1.4 + - - -
107D ASP* 2.9 43.2 + - - +
108D PHE* 4.7 3.0 - - - +
109D ILE* 3.9 27.0 - - - +
----------------------------------------------------------
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