Contacts of the helix formed by residues 628 - 639 (chain D) in PDB entry 1GZL
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 TRP 628 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B TRP* 3.6 31.5 - + - -
36B GLY* 3.6 22.7 - - - -
39B GLN* 3.3 24.1 + - + -
40B LEU* 4.2 24.9 - - + -
43B ARG* 3.0 33.9 - - - +
629D GLU* 1.3 60.5 + - - +
630D GLU* 3.1 11.3 - - - +
631D TRP* 2.9 67.6 + + - +
632D ASP* 3.0 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 629 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628D TRP* 1.3 75.7 - - - +
630D GLU* 1.3 62.9 + - - +
632D ASP* 3.8 6.2 - - - +
633D ARG* 3.4 19.1 + - - +
1640D N2P 1.3 58.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 630 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628D TRP 4.2 4.7 - - - +
629D GLU* 1.3 80.5 - - - +
631D TRP* 1.3 51.2 + - - +
633D ARG* 3.2 13.0 + - - +
634D GLU* 2.7 70.9 + - - +
637D ASN* 5.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 631 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.1 46.0 + - + -
33B THR* 4.9 11.4 - - + -
35B TRP* 3.5 32.0 - + + -
36B GLY* 4.7 4.5 - - - -
628D TRP* 3.0 48.1 - + - +
630D GLU* 1.3 77.9 - - - +
632D ASP* 1.3 76.9 + - + +
634D GLU* 3.5 5.5 - - - +
635D ILE* 2.9 61.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 632 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628D TRP 3.0 13.2 + - - +
629D GLU* 3.9 12.8 - - - +
630D GLU 3.3 0.4 - - - -
631D TRP* 1.3 91.5 - - + +
633D ARG* 1.3 58.7 + - - +
635D ILE* 4.3 3.9 - - - +
636D GLU* 3.1 23.7 + - - +
1640D N2P 2.6 54.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 633 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629D GLU 3.4 11.0 + - - +
630D GLU* 3.2 17.6 + - - +
631D TRP 3.1 0.4 - - - -
632D ASP* 1.3 79.0 + - - +
634D GLU* 1.3 59.9 + - - +
635D ILE 3.4 0.2 - - - -
636D GLU* 2.6 25.1 + - - +
637D ASN* 2.6 53.4 + - - +
1640D N2P 2.8 54.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 634 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 5.6 3.7 - - - +
32B LEU* 3.4 31.6 - - + +
630D GLU* 2.7 49.3 + - - +
631D TRP* 3.1 4.5 + - - +
633D ARG* 1.3 70.9 - - - +
635D ILE* 1.3 66.6 + - - +
637D ASN* 3.3 10.4 + - - +
638D TYR* 3.1 48.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 635 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 3.8 13.5 - - + +
32B LEU* 3.4 36.8 - - + +
33B THR* 4.8 5.4 - - + +
631D TRP* 2.9 54.3 + - + +
632D ASP* 4.3 4.7 - - - +
634D GLU* 1.3 75.4 - - - +
636D GLU* 1.3 55.5 + - + +
638D TYR 3.0 2.3 + - - -
639D THR* 2.6 56.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 636 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632D ASP 3.1 15.1 + - - +
633D ARG* 2.6 40.0 + - - +
634D GLU 3.3 0.2 - - - -
635D ILE* 1.3 81.9 - - + +
637D ASN* 1.3 59.9 + - - +
639D THR* 2.7 27.8 - - - +
1640D N2P 1.3 53.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 637 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 5.6 0.7 - - - +
630D GLU* 5.8 0.6 + - - -
633D ARG* 2.6 48.5 + - - +
634D GLU* 3.7 14.0 + - - +
636D GLU* 1.3 75.7 - - - +
638D TYR* 1.3 67.6 + - + +
639D THR 4.9 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 638 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLU* 5.3 1.9 - - - +
24B ALA 5.1 0.4 - - - -
25B ARG* 3.3 54.7 + - + +
28B LYS* 3.2 48.5 - - + +
29B LEU* 3.4 32.1 - - + +
32B LEU* 4.5 3.6 - - + -
634D GLU* 3.1 45.3 + - - +
635D ILE 3.0 2.2 + - - +
637D ASN* 1.3 82.3 - - + +
639D THR* 1.3 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 639 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 3.2 24.7 - - + +
635D ILE* 2.6 32.0 + - + +
636D GLU* 2.7 22.1 - - - +
637D ASN 4.8 1.3 - - - -
638D TYR* 1.3 76.7 - - - +
----------------------------------------------------------
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