Contacts of the helix formed by residues 576 - 595 (chain B) in PDB entry 4TQ1
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 ALA 576 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B GLN 4.3 0.8 + - - -
575B THR* 1.3 79.6 - - - +
577B ALA* 1.3 65.9 + - - +
578B TRP* 3.4 36.8 - - + +
579B ARG* 3.1 15.2 + - + +
580B LYS* 3.1 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 577 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A MET* 3.6 19.5 - - + -
575B THR 3.6 2.4 + - - -
576B ALA* 1.3 71.8 - - - +
578B TRP* 1.3 63.1 + - - +
579B ARG 3.2 0.2 + - - -
580B LYS* 3.3 11.7 + - - +
581B GLN* 3.0 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 578 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A MET* 3.5 21.4 + - + +
248A GLU* 4.1 11.8 - - + +
249A THR* 3.5 39.0 + - + +
250A PRO* 3.3 31.6 - - + +
253A TRP* 3.6 58.1 - + + -
576B ALA* 3.4 27.9 - - + +
577B ALA* 1.3 78.4 - - - +
579B ARG* 1.3 106.5 + - + +
581B GLN* 3.4 3.6 + - - +
582B ILE* 3.2 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 579 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP* 5.5 6.8 - - - +
4A ASP* 2.3 45.2 + - - -
253A TRP* 3.4 18.9 - - + +
575B THR* 3.7 21.2 - - + +
576B ALA* 3.1 13.2 + - + +
578B TRP* 1.3 116.7 - - + +
580B LYS* 1.3 66.7 + - - +
582B ILE* 3.1 9.8 + - - +
583B PHE* 3.0 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 580 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B GLN* 3.5 18.2 - - - +
575B THR* 3.1 46.0 + - + +
576B ALA 3.1 8.9 + - - +
577B ALA* 3.6 12.4 - - - +
579B ARG* 1.3 76.5 - - - +
581B GLN* 1.3 58.1 + - + +
583B PHE* 3.3 6.5 + - - +
584B GLN* 3.0 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 581 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PRO* 5.8 0.4 - - + -
246A MET* 3.7 31.7 - - + +
577B ALA* 3.0 16.9 + - + +
578B TRP 3.6 9.2 - - - +
579B ARG 3.2 0.2 - - - -
580B LYS* 1.3 75.2 - - + +
582B ILE* 1.3 65.4 + - + +
584B GLN* 4.1 15.9 + - - +
585B GLN* 2.9 63.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 582 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.3 10.8 - - + -
243A ILE* 3.9 22.4 - - + -
245A PRO* 3.9 31.0 - - + -
249A THR* 4.9 2.2 - - - +
253A TRP* 4.0 37.7 - - + -
254A LEU* 4.9 1.1 - - + -
258A LEU* 4.6 5.4 - - + -
578B TRP* 3.2 22.1 + - + +
579B ARG* 3.1 8.8 + - - +
581B GLN* 1.3 76.1 - - - +
583B PHE* 1.3 61.0 + - + +
585B GLN* 3.9 1.4 - - - +
586B LEU* 3.0 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 583 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP* 3.3 53.6 - - + -
4A ASP* 4.1 5.2 - - - -
6A ASP* 4.7 7.2 - - + -
7A VAL* 3.4 24.0 - - + -
10A ASP* 5.7 3.4 - - - -
253A TRP* 5.2 1.3 - + - -
579B ARG* 3.0 50.4 + - + -
580B LYS* 3.9 6.7 - - - +
582B ILE* 1.3 82.1 - - + +
584B GLN* 1.3 57.7 + - + +
586B LEU* 3.4 7.6 + - + +
587B THR* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 584 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B LYS* 3.0 43.9 + - - +
581B GLN* 4.0 19.5 + - - +
583B PHE* 1.3 77.6 - - + +
585B GLN* 1.3 59.1 + - + +
587B THR* 3.3 8.5 + - - -
588B GLU* 3.0 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 585 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ILE* 3.7 21.3 - - + +
244A GLU* 2.7 56.8 + - - +
245A PRO* 4.7 0.8 - - - +
246A MET* 5.3 0.6 - - - +
581B GLN* 2.9 49.0 + - - +
582B ILE* 4.0 2.2 - - - +
584B GLN* 1.3 76.4 - - + +
586B LEU* 1.3 57.4 + - - +
588B GLU* 3.3 7.9 + - - +
589B ARG* 2.9 28.8 + - - +
592B ARG* 4.9 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 586 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.2 21.3 - - + +
10A ASP* 4.1 33.7 - - + +
11A VAL* 4.9 9.6 - - + -
241A HIS* 5.2 1.6 - - + +
243A ILE* 4.0 23.6 - - + -
258A LEU* 5.4 0.4 - - + -
582B ILE* 3.0 38.3 + - + +
583B PHE* 3.9 6.5 - - + +
584B GLN 3.3 0.2 - - - -
585B GLN* 1.3 74.0 - - - +
587B THR* 1.3 65.7 + - - +
589B ARG* 3.2 35.4 + - - +
590B THR* 3.1 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 587 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B PHE* 3.0 15.6 + - - +
584B GLN* 3.5 11.8 - - - -
586B LEU* 1.3 78.1 - - - +
588B GLU* 1.3 71.2 + - - +
590B THR* 3.5 6.9 + - - -
591B LYS* 3.5 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 588 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B GLN* 3.0 22.8 + - + +
585B GLN* 3.7 8.1 - - - +
587B THR* 1.3 80.0 - - - +
589B ARG* 1.3 58.7 + - - +
591B LYS* 2.8 38.6 + - - +
592B ARG* 2.9 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 589 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASP* 2.8 35.2 + - - +
11A VAL* 4.2 3.4 + - - +
14A GLY* 3.7 15.7 - - - -
41A ARG* 3.4 19.5 - - - +
241A HIS* 2.9 41.5 + - - +
242A GLY 4.4 1.6 - - - -
243A ILE* 4.0 9.4 - - + -
585B GLN 2.9 17.6 + - - +
586B LEU* 3.2 21.6 + - - +
588B GLU* 1.3 76.7 - - - +
590B THR* 1.3 62.6 + - - +
592B ARG* 3.6 23.1 - - - +
593B GLU* 2.8 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 590 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASP* 5.4 7.1 + - - +
586B LEU 3.1 13.0 + - - -
587B THR* 3.7 10.9 - - - -
588B GLU 3.3 0.2 - - - -
589B ARG* 1.3 83.1 + - - +
591B LYS* 1.3 62.2 + - + +
593B GLU* 5.3 0.7 - - - -
594B LEU* 3.0 50.2 + - + +
595B GLU 4.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 591 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B THR* 3.5 25.1 + - + +
588B GLU* 2.8 41.7 + - - +
590B THR* 1.3 81.2 - - + +
592B ARG* 1.3 63.1 + - - +
595B GLU* 3.0 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 592 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 3.8 15.1 - - + +
242A GLY* 3.2 25.9 + - - -
243A ILE* 5.0 0.4 - - - +
585B GLN 4.9 2.4 + - - -
588B GLU* 2.9 37.6 + - - +
589B ARG* 3.1 25.1 + - - +
591B LYS* 1.3 79.3 - - - +
593B GLU* 1.3 69.0 + - + +
594B LEU 3.8 0.3 + - - -
595B GLU* 4.8 0.5 + - - +
597B PHE* 4.1 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 593 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG 3.2 23.9 + - - +
16A ILE* 4.1 4.6 - - - +
17A PRO* 3.1 28.4 - - + +
41A ARG* 2.8 45.3 + - - -
87A PHE* 4.6 6.4 - - - -
96A LEU* 4.1 13.5 - - + +
242A GLY* 4.9 0.2 - - - -
589B ARG* 2.8 45.8 + - + +
590B THR* 5.3 0.4 - - - -
592B ARG* 1.3 87.2 + - + +
594B LEU* 1.3 69.2 + - + +
597B PHE* 3.7 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 594 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE 5.8 2.2 - - - +
15A ARG* 4.3 20.2 - - + -
38A LEU* 4.1 28.5 - - + -
590B THR* 3.0 33.1 + - + +
593B GLU* 1.3 89.9 - - + +
595B GLU* 1.3 64.7 + - - +
596B ASN 3.3 2.9 - - - -
597B PHE* 3.1 14.3 + - - -
598B ARG* 3.2 34.1 + - + +
602B GLN* 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 595 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B THR 4.0 1.0 + - - -
591B LYS* 3.0 38.5 + - + +
592B ARG 4.8 0.4 - - - +
593B GLU 4.1 0.2 - - - -
594B LEU* 1.3 76.8 - - - +
596B ASN* 1.3 67.1 + - + +
597B PHE* 3.3 0.6 + - - -
598B ARG* 3.1 41.5 + - - +
----------------------------------------------------------
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