Contacts of the helix formed by residues 590 - 607 (chain B) in PDB entry 4D1Q
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 GLY 590 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ARG* 3.9 5.6 - - - -
588B ARG 3.2 4.9 + - - -
589B ILE* 1.3 73.3 - - - +
591B GLN* 1.3 74.7 + - - +
592B GLN* 3.2 3.8 - - - -
593B THR* 2.9 14.6 + - - -
594B VAL* 3.0 9.7 + - - -
7C C 2.9 18.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 591 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ARG* 4.0 24.2 - - - +
191B PHE* 4.3 15.3 - - + -
211B LEU 4.8 3.4 - - - +
212B LYS* 5.7 3.6 - - + +
213B SER* 3.2 38.1 + - - +
215B ASP* 4.1 11.1 - - - +
216B PHE* 5.9 2.9 - - - -
589B ILE 4.1 0.2 + - - -
590B GLY* 1.3 71.4 - - - -
592B GLN* 1.3 82.6 + - + +
594B VAL* 2.7 19.5 + - - +
595B ASP* 2.7 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 592 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B THR* 4.1 22.0 - - + +
156B LYS* 5.2 5.2 + - - -
212B LYS* 5.0 14.5 + - - +
590B GLY* 4.4 2.0 - - - +
591B GLN* 1.3 91.3 - - - +
593B THR* 1.3 60.7 + - - +
595B ASP* 3.2 5.8 + - - +
596B SER* 2.6 38.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 593 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE* 3.4 36.6 - - + -
148B SER* 4.1 8.0 + - - +
151B VAL* 5.5 0.9 - - + -
152B THR* 4.4 10.2 + - - +
589B ILE* 3.5 18.6 - - + -
590B GLY* 2.9 9.3 + - - -
592B GLN* 1.3 77.9 - - - +
594B VAL* 1.3 58.2 + - - +
596B SER* 3.2 5.7 + - - -
597B LEU* 2.7 38.8 + - + +
7C C 2.7 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 594 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B PHE* 5.0 5.2 - - + -
211B LEU* 4.0 14.1 - - + -
578B ALA* 4.8 2.2 - - + -
581B ILE* 4.1 11.7 - - + -
582B ILE* 3.8 37.2 - - + -
589B ILE* 3.9 22.2 - - + +
590B GLY 3.0 12.3 + - - +
591B GLN* 2.7 16.6 + - - +
593B THR* 1.3 72.3 - - - +
595B ASP* 1.3 62.6 + - - +
597B LEU* 3.2 6.2 + - - +
598B LEU* 2.9 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 595 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LYS* 3.6 30.1 + - - +
209B LEU 4.2 1.1 - - - +
210B GLY* 3.2 13.4 - - - -
211B LEU* 3.1 40.5 + - - +
212B LYS* 3.2 28.2 + - - +
591B GLN* 2.7 14.5 + - + +
592B GLN* 3.6 7.6 - - - +
594B VAL* 1.3 72.7 - - - +
596B SER* 1.3 59.3 + - - +
598B LEU* 3.3 6.3 + - - +
599B PHE* 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 596 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL* 3.8 16.8 - - - -
152B THR* 3.8 13.1 - - - +
155B ALA* 3.5 31.9 - - - +
159B LYS* 5.1 1.2 + - - -
592B GLN 2.6 22.9 + - - -
593B THR* 3.4 5.4 - - - -
595B ASP* 1.3 75.9 + - - +
597B LEU* 1.3 68.6 + - - +
598B LEU 2.8 1.6 + - - -
599B PHE* 2.9 2.5 + - - -
600B LEU* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 597 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 4.1 24.5 - - + +
103A VAL* 4.1 25.4 - - + +
106A CYS* 5.8 2.2 - - - -
107A ARG 5.4 0.4 - - - +
109A PHE* 3.5 15.5 - - + -
151B VAL* 3.8 11.4 - - + +
581B ILE* 3.9 28.4 - - + +
586B ARG* 4.8 5.6 - - - +
589B ILE* 4.3 4.5 - - + -
593B THR* 2.7 52.1 + - + +
594B VAL* 3.5 4.5 - - - +
596B SER* 1.3 72.9 - - - +
598B LEU* 1.3 61.4 + - - +
600B LEU* 4.9 2.2 - - - -
601B ASN* 3.3 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 598 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 4.6 19.5 - - + +
210B GLY 6.3 0.2 - - - -
211B LEU* 3.4 41.7 - - + -
574B THR* 4.6 12.6 - - + -
577B LEU* 4.1 13.7 - - + -
578B ALA* 4.0 20.0 - - + +
581B ILE* 3.3 25.8 - - + -
594B VAL* 2.9 26.4 + - + +
595B ASP* 3.4 4.7 - - - +
596B SER 2.8 3.6 + - - -
597B LEU* 1.3 73.6 - - - +
599B PHE* 1.3 64.3 + - - +
601B ASN* 3.4 6.2 + - + +
602B SER* 3.2 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 599 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ALA* 4.3 6.1 - - + -
158B LYS* 4.1 8.3 - - + -
159B LYS* 3.3 56.3 - - + -
162B ILE* 3.9 18.4 - - + -
207B LEU* 5.1 5.8 - - + -
208B ILE* 3.5 28.4 - - + +
209B LEU* 4.2 7.4 - - - +
235B PHE* 3.9 16.4 - + - -
595B ASP* 2.8 28.3 + - - +
596B SER* 3.6 3.6 - - - +
598B LEU* 1.3 71.7 - - - +
600B LEU* 1.3 76.9 + - + +
602B SER* 3.2 3.9 + - - -
603B PHE* 2.8 37.5 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 600 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 3.5 25.6 - - + -
151B VAL* 3.4 31.6 - - + +
154B ASP* 3.9 25.1 - - + +
155B ALA* 3.5 17.7 - - + +
158B LYS* 4.2 7.9 - - + -
596B SER 2.8 30.4 + - - +
599B PHE* 1.3 78.1 - - + +
601B ASN* 1.3 66.3 + - - +
603B PHE* 2.9 5.4 + - + +
604B TYR* 2.8 55.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 601 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 3.3 29.6 + - - +
104A ARG* 3.6 23.4 + - - +
106A CYS* 6.1 1.3 - - - +
577B LEU* 5.0 9.7 - - - +
597B LEU 3.3 17.6 + - - +
598B LEU* 3.4 6.7 + - + +
599B PHE 3.2 0.4 - - - -
600B LEU* 1.3 80.1 - - - +
602B SER* 1.3 60.6 + - - +
604B TYR* 3.6 3.9 + - - +
605B LYS* 3.2 50.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 602 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ASP 3.8 1.7 + - - -
207B LEU* 3.1 19.7 - - - +
208B ILE* 2.9 44.9 + - - +
598B LEU 3.2 13.2 + - - -
599B PHE 3.5 7.0 - - - -
600B LEU 3.1 0.6 - - - -
601B ASN* 1.3 72.7 - - - +
603B PHE* 1.3 67.8 + - - +
605B LYS* 3.1 13.2 + - - +
606B ASN* 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 603 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LYS* 3.7 41.3 - - + -
161B LEU* 5.1 8.3 - - + -
162B ILE* 3.2 31.4 - - + -
207B LEU* 4.2 9.6 - - - +
599B PHE* 2.8 29.7 + + + +
600B LEU* 3.2 9.4 - - - +
602B SER* 1.3 74.1 - - - +
604B TYR* 1.3 92.4 + + - +
606B ASN* 2.9 3.6 + - - -
607B PHE* 2.7 66.0 + + + +
608B CYS* 4.5 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 604 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLN* 3.4 39.3 + - + +
103A VAL* 4.2 18.9 - - + +
104A ARG* 3.4 38.1 - - + +
154B ASP* 3.3 23.0 + - - -
158B LYS* 4.1 12.0 - - - -
600B LEU* 2.8 39.9 + - + +
601B ASN 3.8 5.4 - - - +
603B PHE* 1.3 99.4 - + - +
605B LYS* 1.3 59.7 + - - +
607B PHE 4.2 0.4 - - - -
608B CYS* 3.5 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 605 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 6.0 1.8 - - - +
577B LEU* 4.6 16.2 - - - +
601B ASN* 3.2 40.7 + - - +
602B SER* 3.1 13.4 + - - +
604B TYR* 1.3 78.1 - - - +
606B ASN* 1.3 68.0 + - - +
607B PHE 3.8 0.2 + - - -
608B CYS 4.1 9.5 - - - +
2E G 4.7 0.6 + - - -
3E A 3.2 47.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 606 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU 4.4 2.4 - - - +
205B ARG* 3.1 40.2 + - - +
206B ASP* 2.6 44.7 + - - +
207B LEU* 3.2 24.1 - - + +
602B SER* 2.9 18.5 + - - +
603B PHE 3.9 1.3 - - - +
605B LYS* 1.3 83.9 - - - +
607B PHE* 1.3 73.7 + - + +
608B CYS 3.7 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 607 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 3.4 35.9 - - + -
165B GLU* 4.0 14.4 - - + -
166B ILE* 5.9 0.9 - - + -
198B TYR* 3.6 18.6 - - - -
205B ARG* 3.6 33.2 - - - -
207B LEU* 4.7 13.0 - - + -
603B PHE* 2.7 56.4 + + + +
606B ASN* 1.3 88.5 - - + +
608B CYS* 1.3 68.5 + - - +
609B LYS* 5.3 1.7 - - - -
----------------------------------------------------------
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