Contacts of the strand formed by residues 715 - 722 (chain B) in PDB entry 1GGT
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 715 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ASN* 2.7 41.6 + - - -
282B ILE 4.0 11.7 + - - -
283B TYR* 3.7 8.5 - - - -
288B PRO* 3.8 14.2 - - - +
290B SER* 3.9 17.0 - - - -
600B GLU* 3.0 47.3 + - + +
629B ILE* 4.4 3.5 - - - +
709B MET* 3.9 9.2 - - - -
710B SER* 3.5 28.3 + - - +
711B SER 3.6 16.3 + - - -
712B ASP* 4.4 12.1 + - - +
713B SER 4.6 6.6 + - - +
714B LEU* 1.3 90.0 - - - +
716B HIS* 1.3 72.8 + - - +
717B VAL* 3.6 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 716 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B TYR* 3.5 37.1 + + - -
290B SER* 2.8 36.0 + - - +
315B TRP* 4.1 12.3 - + - -
372B TYR* 4.7 0.8 + - - -
600B GLU 3.6 11.4 - - - +
601B GLN* 3.5 42.6 - - + +
629B ILE* 3.8 19.6 - - + +
709B MET 3.7 4.2 + - - -
715B ARG* 1.3 83.4 - - + +
717B VAL* 1.3 60.0 - - - +
718B TYR* 3.3 31.6 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 717 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B ILE* 3.8 25.8 - - + -
630B PRO 3.6 19.5 - - - +
632B ILE* 3.3 26.2 - - + -
652B PHE* 4.3 11.4 - - + -
708B SER* 3.0 4.9 - - - -
709B MET* 3.0 57.4 + - + +
714B LEU* 4.2 7.9 - - + -
715B ARG 4.3 2.5 - - - -
716B HIS* 1.3 78.9 - - - +
718B TYR* 1.3 71.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 718 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B TYR* 3.7 18.4 - + - -
223B ARG* 3.4 57.7 + - + -
224B SER 6.0 0.2 - - - +
290B SER* 2.8 30.4 + - - -
292B TRP 4.5 0.2 - - - -
293B THR* 5.8 0.2 - - + -
315B TRP* 5.2 0.2 - - - -
630B PRO 5.9 0.2 - - - -
631B GLU* 3.5 12.2 - - - +
632B ILE* 3.0 22.3 + - - -
706B ILE* 6.0 1.6 - - + -
707B ALA 3.1 11.9 - - - +
708B SER* 3.4 18.8 - - - +
709B MET 5.9 0.2 - - - -
716B HIS* 3.3 53.0 + + - -
717B VAL* 1.3 86.5 - - - +
719B GLY* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 719 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B GLU* 5.2 4.7 - - - -
632B ILE* 3.7 23.5 - - - +
634B ILE* 4.3 5.8 - - - -
706B ILE* 3.6 2.4 - - - +
707B ALA* 2.8 33.2 + - - +
718B TYR* 1.3 79.5 - - - +
720B GLU* 1.3 63.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 720 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B VAL* 5.6 1.6 - - - +
222B THR* 5.3 2.9 + - - +
223B ARG* 4.1 5.9 - - - -
224B SER* 3.3 34.8 + - - -
472B ASP* 4.2 3.6 - - - +
632B ILE 4.9 0.6 + - - +
634B ILE* 4.2 10.6 + - - +
704B LYS* 2.8 38.0 + - + +
705B LEU 3.1 15.9 - - - +
706B ILE* 4.7 1.1 - - + -
719B GLY* 1.3 75.5 - - - +
721B LEU* 1.3 63.1 + - - +
722B ASP* 4.3 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 721 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B ILE* 3.5 39.0 - - + +
635B LYS* 4.0 1.1 - - - -
636B VAL* 3.7 41.1 - - + +
704B LYS* 3.1 4.8 - - - -
705B LEU* 2.8 32.1 + - + +
720B GLU* 1.3 78.7 - - - +
722B ASP* 1.3 98.2 + - - +
723B VAL* 3.6 9.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 722 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B ASP* 3.9 5.4 - - - +
702B HIS* 2.8 39.4 + - + +
703B ARG 3.1 7.2 - - - -
704B LYS* 2.9 31.6 + - - +
720B GLU* 4.3 2.8 - - - +
721B LEU* 1.3 90.1 - - - +
723B VAL* 1.3 60.0 + - - +
724B GLN 4.2 0.2 + - - -
----------------------------------------------------------
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