Contacts of the helix formed by residues 641 - 648 (chain A) in PDB entry 6RQT
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 641 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A TYR* 3.3 21.1 - - - +
508A PRO 5.8 0.2 - - - +
640A ASN* 1.3 75.2 - - - +
642A ASN* 1.3 65.1 + - - +
643A ALA 3.1 3.1 - - - -
644A ARG* 3.0 35.6 + - - +
645A ALA* 3.3 4.7 + - - +
95F GLY* 2.9 16.7 - - - +
98F ALA* 3.3 19.2 - - - +
99F LEU* 2.6 51.3 + - + +
102F SER* 5.6 2.2 - - - +
117F PRO* 4.5 10.8 - - + +
118F LEU* 4.6 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A ASN* 3.7 0.4 - - - +
641A GLU* 1.3 84.8 - - - +
643A ALA* 1.3 57.4 + - - +
645A ALA* 3.4 18.8 - - - +
646A GLU* 3.6 9.4 - - - +
1086B PHE* 3.4 39.5 - - + +
91F ALA 4.7 6.4 - - - +
92F ARG* 4.3 20.0 + - - +
95F GLY* 3.2 31.6 + - - -
96F THR* 4.0 7.3 + - - +
99F LEU* 3.9 17.9 - - + +
109G PRO 5.7 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 643 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A PRO* 3.6 26.6 - - + +
640A ASN 5.1 1.3 - - - +
641A GLU* 3.1 1.0 - - - +
642A ASN* 1.3 76.0 - - - +
644A ARG* 1.3 58.8 + - - +
645A ALA 3.2 0.7 - - - -
646A GLU* 3.0 30.8 - - - +
647A ALA* 3.1 20.3 + - - +
1086B PHE* 3.2 30.2 - - + +
1087B LEU* 4.3 5.4 - - + -
1090B ASP* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A TYR* 3.4 39.2 + - + -
582A LYS* 5.7 0.6 - - - +
584A ARG 2.7 29.0 + - - -
585A ASP* 3.8 19.3 - - + +
586A VAL* 4.5 10.7 - - + +
637A PHE* 6.3 0.4 - - + -
638A PRO* 4.5 13.2 - - + -
640A ASN 4.0 9.6 + - - +
641A GLU* 3.0 18.9 + - - +
643A ALA* 1.3 77.6 - - - +
645A ALA* 1.3 61.7 + - - +
647A ALA 4.2 0.2 - - - -
648A LEU* 3.3 33.2 + - + +
116F ASP* 4.4 16.1 + - - +
117F PRO* 4.5 8.2 - - - +
118F LEU* 3.5 45.1 - - - +
119F ARG* 5.6 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A GLU 3.3 4.9 + - - +
642A ASN* 3.4 22.4 - - - +
643A ALA 3.2 0.6 - - - -
644A ARG* 1.3 82.0 - - - +
646A GLU* 1.3 59.3 + - + +
648A LEU* 4.3 1.7 - - - +
649A ASN* 3.3 23.6 + - - +
90F ARG 5.6 0.5 - - - +
91F ALA* 5.3 9.7 - - - +
94F LEU* 4.8 8.2 - - + +
95F GLY* 4.0 14.4 - - - +
118F LEU* 3.7 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A ASN 3.6 15.5 - - - +
643A ALA* 3.0 24.0 - - - +
645A ALA* 1.3 76.9 - - - +
647A ALA* 1.3 67.6 + - - +
648A LEU 3.2 2.0 - - - -
649A ASN* 2.9 1.3 + - - +
650A LEU* 2.4 40.7 + - + +
651A ALA* 5.3 0.7 + - - +
1651A THR* 5.3 1.6 - - + -
1084B THR* 2.7 43.8 + - - +
1086B PHE* 4.9 4.7 - - + -
1087B LEU* 3.2 30.6 - - - +
91F ALA* 4.2 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A VAL* 3.8 26.0 - - + +
588A LEU* 5.4 7.4 - - + -
602A GLY* 4.3 3.5 - - - -
638A PRO* 5.4 2.9 - - + -
643A ALA 3.1 20.8 + - - +
646A GLU* 1.3 89.2 - - - +
648A LEU* 1.3 58.7 + - - +
651A ALA* 3.9 18.5 + - + +
652A ASN* 3.8 15.8 + - - -
1087B LEU* 4.6 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 648 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A ARG 5.6 3.8 - - - +
585A ASP* 5.8 0.4 - - - -
586A VAL* 3.6 25.2 - - + +
604A LYS* 5.1 17.5 - - - +
644A ARG* 3.3 29.2 + - - +
645A ALA 4.3 1.6 - - - +
646A GLU 3.2 0.4 - - - -
647A ALA* 1.3 76.9 - - - +
649A ASN* 1.3 64.5 + - + +
650A LEU 3.8 0.2 - - - -
652A ASN* 3.4 27.7 + - - +
118F LEU* 4.6 5.2 - - + -
119F ARG* 3.5 36.1 - - - +
122F MET* 5.7 0.9 - - - -
----------------------------------------------------------
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