Contacts of the helix formed by residues 712 - 727 (chain A) in PDB entry 2G5T
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 HIS 712 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A ILE* 3.3 38.0 - - + +
238A TYR* 5.4 1.6 - + + -
256A TYR* 3.2 46.5 - + - -
258A LYS* 2.7 31.9 + - - +
661A TYR 4.2 1.4 + - - -
704A HIS* 3.5 1.7 + - - -
708A ASP 3.5 14.4 - - - +
709A ASP* 3.2 18.2 + - - -
710A ASN 3.5 1.5 + - - -
711A VAL* 1.3 73.2 - - - +
713A PHE* 1.3 68.5 + - - +
714A GLN* 4.0 16.4 - - + +
715A GLN* 2.8 28.0 + - + +
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Residues in contact with PHE 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A TYR* 6.2 2.7 - - + -
704A HIS* 3.7 40.5 - - + -
705A GLY 3.8 6.7 - - - +
706A THR* 3.8 39.5 + - + +
708A ASP* 4.2 5.1 + - - +
711A VAL 3.6 2.2 + - - -
712A HIS* 1.3 70.6 - - - +
714A GLN* 1.3 64.2 + - - +
716A SER* 2.8 16.8 + - - -
717A ALA* 3.0 17.1 + - + -
734A TRP* 3.9 15.5 - + + -
241B TYR* 3.5 25.1 - + + +
706B THR* 5.0 8.3 - - + -
713B PHE* 6.0 2.9 - + - -
734B TRP* 3.8 45.5 - + + -
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Residues in contact with GLN 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LYS* 2.9 29.5 + - - -
661A TYR* 3.4 27.8 + - + +
712A HIS* 2.9 10.2 + - + +
713A PHE* 1.3 76.3 - - - +
715A GLN* 1.3 61.3 + - - +
717A ALA* 3.1 3.2 + - - +
718A GLN* 3.0 28.6 + - + +
241B TYR* 3.5 33.1 + - + -
246B LEU 3.4 15.4 + - - -
247B GLN 3.0 21.5 + - - +
249B PRO* 3.6 28.1 - - + +
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Residues in contact with GLN 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A PRO 3.4 16.6 - - - +
656A VAL* 3.3 13.8 - - - +
657A SER* 2.8 55.9 + - - +
658A ARG 3.5 9.4 + - - +
661A TYR* 3.5 40.7 + - + +
662A TYR* 4.0 17.4 - - - +
704A HIS* 4.7 0.2 - - - +
711A VAL* 3.7 19.2 - - + +
712A HIS* 2.8 27.2 + - + +
714A GLN* 1.3 73.9 - - - +
716A SER* 1.3 60.2 + - - +
718A GLN* 3.5 0.9 + - - +
719A ILE* 3.4 11.0 + - - +
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Residues in contact with SER 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A PRO* 3.6 4.9 + - - +
702A LEU* 3.1 38.9 - - - +
704A HIS* 2.8 39.7 - - - +
713A PHE* 2.8 9.1 + - - -
715A GLN* 1.3 74.0 - - - +
717A ALA* 1.3 66.3 + - - +
719A ILE* 3.1 7.4 + - - +
720A SER* 3.0 23.4 + - - -
734B TRP* 4.0 8.7 - - - -
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Residues in contact with ALA 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713A PHE* 3.0 17.8 + - + +
714A GLN* 3.3 13.0 - - - +
716A SER* 1.3 78.0 - - - +
718A GLN* 1.3 59.3 + - - +
720A SER* 3.0 10.0 + - - -
721A LYS* 3.2 5.2 + - - +
241B TYR* 4.0 26.9 - - + -
734B TRP* 4.1 5.5 - - - +
736B THR* 2.7 42.4 + - + +
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Residues in contact with GLN 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A TYR* 3.1 30.8 + - + +
689A MET* 3.6 26.2 - - + +
714A GLN* 3.0 22.4 + - + +
715A GLN 3.5 1.8 + - - +
716A SER 3.2 0.2 - - - -
717A ALA* 1.3 73.9 - - - +
719A ILE* 1.3 66.3 + - - +
721A LYS* 3.0 33.0 - - - +
722A ALA* 3.0 24.3 + - - +
241B TYR* 3.6 18.3 - - + +
242B SER 3.0 17.9 + - - +
243B ASP 3.8 0.7 - - - +
244B GLU* 3.8 16.2 - - - +
246B LEU 5.1 1.4 - - - +
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Residues in contact with ILE 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A SER* 4.3 2.7 - - - +
655A PRO* 3.9 22.7 - - + -
657A SER* 3.5 23.8 - - - -
688A VAL* 4.1 22.0 - - + -
689A MET* 4.0 9.6 - - - +
695A PHE* 5.6 0.4 - - + -
700A TYR* 3.6 40.2 - - + +
702A LEU* 4.2 5.6 - - + -
715A GLN 3.4 12.5 + - - +
716A SER* 3.1 10.6 + - - +
718A GLN* 1.3 77.7 - - - +
720A SER* 1.3 63.7 + - - +
722A ALA* 3.2 6.1 + - - +
723A LEU* 3.0 30.4 + - + +
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Residues in contact with SER 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A LEU* 4.4 1.1 - - - -
716A SER 3.0 9.7 + - - -
717A ALA 3.0 2.3 + - - -
719A ILE* 1.3 77.5 - - - +
721A LYS* 1.3 55.7 + - - +
723A LEU* 3.3 2.5 + - - +
724A VAL* 2.9 37.6 + - - +
730A PHE* 3.7 30.7 - - - -
734B TRP* 2.9 26.5 + - - -
736B THR* 2.8 34.1 - - - +
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Residues in contact with LYS 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717A ALA 3.2 12.0 + - - +
718A GLN* 3.0 33.7 - - - +
719A ILE 3.2 0.2 - - - -
720A SER* 1.3 80.9 + - - +
722A ALA* 1.3 58.0 + - - +
724A VAL* 3.5 5.8 + - + +
725A ASP* 2.9 51.2 + - - +
241B TYR* 5.1 0.4 - - - -
242B SER 3.1 21.7 + - - +
243B ASP* 4.2 8.9 + - - +
244B GLU* 4.3 1.4 - - - +
736B THR* 3.7 35.7 - - + +
737B ASP* 3.9 12.8 - - + +
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Residues in contact with ALA 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689A MET* 3.4 44.9 - - + +
692A ALA* 3.6 6.3 - - + +
718A GLN 3.0 11.3 + - - +
719A ILE 3.2 4.7 + - - +
721A LYS* 1.3 74.1 - - - +
723A LEU* 1.3 66.1 + - - +
725A ASP* 3.5 7.9 + - - +
726A VAL* 3.2 24.6 + - - +
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Residues in contact with LEU 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692A ALA* 3.8 16.8 - - + +
695A PHE* 3.6 39.5 - - + -
700A TYR* 3.6 35.9 - - + -
719A ILE* 3.0 23.8 + - + +
720A SER 3.7 2.0 - - - +
721A LYS 3.3 0.2 - - - -
722A ALA* 1.3 73.0 - - - +
724A VAL* 1.3 64.8 + - - +
726A VAL* 3.2 5.9 + - - +
727A GLY 3.0 4.7 + - - -
728A VAL* 2.9 34.6 + - + +
730A PHE* 3.7 37.0 - - + -
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Residues in contact with VAL 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720A SER* 2.9 23.9 + - - +
721A LYS* 3.8 7.4 - - + +
723A LEU* 1.3 74.9 - - - +
725A ASP* 1.3 60.7 + - - +
727A GLY* 2.9 18.9 + - - -
730A PHE* 4.2 7.9 - - + -
734B TRP 5.9 0.9 - - - +
735B TYR* 3.9 21.5 - - + -
746B THR* 3.6 19.0 - - - +
747B ALA* 3.7 35.9 - - + +
750B HIS* 3.8 30.4 - - + +
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Residues in contact with ASP 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721A LYS* 2.9 42.8 + - - +
722A ALA* 3.9 7.7 - - - +
724A VAL* 1.3 77.6 - - - +
726A VAL* 1.3 58.5 + - - +
727A GLY 3.4 0.2 - - - -
746B THR* 3.0 37.2 + - + +
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Residues in contact with VAL 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692A ALA* 3.8 14.8 - - + +
693A GLU* 3.0 43.0 - - + +
696A LYS* 3.2 18.6 + - - +
722A ALA 3.2 15.0 + - - +
723A LEU* 3.4 7.9 - - - +
724A VAL 3.0 0.8 - - - -
725A ASP* 1.3 77.1 - - - +
727A GLY* 1.3 56.6 + - - +
728A VAL* 3.2 31.2 - - + -
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Residues in contact with GLY 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696A LYS* 3.5 13.8 + - - +
723A LEU 3.0 0.2 + - - -
724A VAL* 2.9 15.4 + - - -
725A ASP 3.4 0.8 - - - -
726A VAL* 1.3 80.9 - - - +
728A VAL* 1.3 59.6 + - - +
729A ASP 4.1 1.0 + - - -
746B THR* 5.8 0.2 - - - +
750B HIS* 5.0 6.1 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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