Contacts of the helix formed by residues 624 - 638 (chain D) in PDB entry 3TIW
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 LEU 624 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D CL 3.3 8.3 - - + +
622D VAL 4.2 0.4 + - - -
623D THR* 1.3 87.3 - - - +
625D ARG* 1.3 70.8 + - + +
626D ARG* 3.6 41.7 - - + +
627D ARG* 3.2 42.9 + - + +
628D MET 3.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 625 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR* 3.4 26.5 + - - +
105B CYS 4.8 0.2 + - - -
106B PRO* 4.6 10.8 + - - +
108B VAL* 2.7 30.5 + - - +
109B LYS* 4.2 5.3 - - - +
110B TYR* 3.8 35.5 - - + +
175B ILE* 3.5 24.5 - - - +
623D THR* 3.4 5.2 + - - -
624D LEU* 1.3 77.2 - - + +
626D ARG* 1.3 64.3 + - - +
628D MET* 2.9 24.8 + - + +
629D LEU* 3.2 17.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 626 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PHE* 3.6 36.0 - - - +
53B ARG* 3.2 23.5 + - - +
54B GLY* 3.4 32.5 - - - +
55B ASP* 3.5 22.4 - - - +
188B CL 3.5 22.8 - - - +
624D LEU* 3.6 26.7 - - + +
625D ARG* 1.3 79.4 - - - +
627D ARG* 1.3 93.0 + - - +
628D MET 3.2 0.2 + - - -
629D LEU* 3.3 3.8 + - - +
630D ALA* 3.0 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 627 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ARG* 4.3 18.1 + - - +
188B CL 3.6 18.7 - - - +
4D CL 3.4 31.0 - - + +
623D THR* 4.7 3.8 - - + -
624D LEU* 3.2 33.1 + - + +
625D ARG 3.1 0.8 - - - -
626D ARG* 1.3 110.2 - - - +
628D MET* 1.3 55.7 + - - +
630D ALA* 4.0 1.8 - - - +
631D ALA* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 628 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR* 4.8 8.3 - - - +
143B TYR* 3.8 48.0 - - + -
623D THR* 4.1 22.4 - - + +
624D LEU 3.5 5.0 + - - +
625D ARG* 2.9 16.0 + - + +
627D ARG* 1.3 77.9 - - - +
629D LEU* 1.3 67.0 + - + +
631D ALA* 3.9 4.9 - - + +
632D ALA* 3.4 22.7 + - - +
635D ARG* 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 629 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLY* 3.9 12.6 - - - +
56B THR* 3.9 12.1 - - + -
70B ILE* 3.7 32.9 - - + +
110B TYR* 5.6 0.7 - - + -
142B ALA 5.0 1.2 - - - +
143B TYR* 3.6 41.5 - - + +
175B ILE* 3.8 27.8 - - + -
625D ARG* 3.2 30.9 + - + +
626D ARG* 3.8 7.2 - - - +
628D MET* 1.3 81.6 - - + +
630D ALA* 1.3 62.5 + - - +
632D ALA* 3.5 3.3 + - - +
633D ALA* 3.2 22.6 + - - +
636D ARG* 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 630 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ARG* 3.7 31.2 - - - +
54B GLY* 3.6 19.9 - - - +
70B ILE* 4.9 0.7 - - - -
72B LEU* 4.1 9.4 - - + -
626D ARG 3.0 16.5 + - - +
627D ARG 4.0 1.6 - - - +
629D LEU* 1.3 76.0 - - - +
631D ALA* 1.3 55.1 + - - +
633D ALA* 3.2 7.1 + - - +
634D GLU* 2.8 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 631 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ARG* 3.9 4.4 - - - +
627D ARG 3.0 20.6 + - - +
628D MET* 3.9 7.2 - - + +
630D ALA* 1.3 77.6 - - - +
632D ALA* 1.3 56.9 + - - +
634D GLU* 3.4 12.3 + - - +
635D ARG* 2.9 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 632 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLU 3.8 15.9 - - - +
142B ALA* 3.9 7.6 - - - +
143B TYR* 4.7 2.2 - - + -
628D MET 3.4 15.4 + - - +
629D LEU* 3.8 4.5 - - - +
630D ALA 3.3 0.6 - - - -
631D ALA* 1.3 75.7 - - - +
633D ALA* 1.3 60.9 + - - +
635D ARG* 3.3 27.7 + - - +
636D ARG* 3.1 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 633 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASN* 5.4 0.5 + - - -
35B ASP* 4.3 2.5 - - - +
38B VAL* 4.0 21.5 - - + -
70B ILE* 4.9 4.5 - - + -
72B LEU* 4.2 13.7 - - + -
629D LEU 3.2 14.4 + - - +
630D ALA* 3.2 10.7 + - - +
632D ALA* 1.3 75.2 - - - +
634D GLU* 1.3 59.5 + - - +
636D ARG* 3.2 26.4 + - - +
637D LEU* 3.0 29.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
64A ARG* 3.1 16.4 + - - -
53B ARG* 2.6 49.3 + - - +
72B LEU* 4.1 21.0 - - + +
630D ALA 2.8 19.1 + - - +
631D ALA* 3.9 7.0 - - - +
633D ALA* 1.3 73.0 - - - +
635D ARG* 1.3 61.0 + - + +
637D LEU* 3.5 14.3 - - + +
638D GLN* 3.4 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 635 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LYS* 6.3 0.7 - - - +
141B GLU* 4.1 16.0 + - - +
143B TYR* 6.0 0.6 - - - -
628D MET 5.6 0.4 + - - -
631D ALA* 2.9 41.2 + - + +
632D ALA* 3.6 28.4 + - - +
633D ALA 3.1 0.2 - - - -
634D GLU* 1.3 76.9 - - + +
636D ARG* 1.3 64.7 + - - +
637D LEU 3.2 1.3 - - - -
638D GLN* 3.4 33.8 + - - +
639D LYS* 3.7 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 636 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASN* 5.7 0.4 - - - -
35B ASP* 2.7 41.0 + - + +
37B SER* 4.1 10.3 - - - -
38B VAL* 4.6 0.4 - - - +
70B ILE* 5.2 4.4 - - - +
142B ALA* 3.1 42.0 + - - +
144B ARG* 3.3 32.0 - - - +
629D LEU 5.2 0.2 + - - -
632D ALA* 3.1 24.2 + - - +
633D ALA* 3.2 20.9 + - - +
635D ARG* 1.3 76.1 - - + +
637D LEU* 1.3 64.8 + - - +
639D LYS* 3.2 21.1 + - - +
640D GLN* 3.5 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 637 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASN* 3.5 46.7 - - + +
35B ASP* 5.6 0.2 + - - -
72B LEU* 4.2 19.5 - - + -
633D ALA 3.0 11.3 + - - +
634D GLU* 3.5 19.3 - - + +
635D ARG 3.2 0.2 - - - -
636D ARG* 1.3 74.4 - - - +
638D GLN* 1.3 57.8 + - + +
639D LYS 2.9 10.3 + - - -
640D GLN* 3.6 22.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 638 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 4.2 10.0 + - - +
93A ARG* 3.2 28.7 + - - +
164A LYS* 4.4 18.8 - - - +
634D GLU 3.4 11.1 + - - +
635D ARG* 3.4 31.5 + - - +
637D LEU* 1.3 75.9 - - - +
639D LYS* 1.3 58.3 + - + +
640D GLN 3.9 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