Contacts of the strand formed by residues 599 - 608 (chain B) in PDB entry 2C11
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 HIS 599 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A THR* 5.1 8.7 - - + +
505A GLY* 6.4 0.9 - - - -
508A GLY 5.0 1.3 - - - -
509A ASN* 3.4 31.9 + - + +
510A GLN* 2.8 42.7 + - - +
566B ARG* 5.7 2.9 + - - -
594B SER* 2.9 5.0 - - - -
595B ASN* 2.7 43.3 + - - +
597B TRP* 3.6 17.7 + - + -
598B GLY* 1.3 79.1 + - - +
600B PRO* 1.3 73.8 - - - +
601B ARG 3.1 0.3 + - - -
709B ASN* 3.6 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 600 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B TRP* 4.2 26.5 - - + +
588B TYR* 4.8 10.4 - - - +
590B ALA* 4.2 7.1 - - + +
591B SER 3.7 18.4 - - - +
592B ASN 5.2 3.1 - - - +
593B HIS 3.5 9.4 - - - +
594B SER* 3.7 6.3 - - - +
598B GLY 4.5 1.8 - - - +
599B HIS* 1.3 88.7 - - + +
601B ARG* 1.3 63.9 + - - +
602B GLY* 3.1 4.5 + - - -
708B TYR* 3.8 1.6 - - - +
709B ASN* 3.8 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 601 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B GLU* 2.9 32.2 + - - -
532B VAL* 3.5 8.8 - - - +
533B ALA* 3.5 23.0 - - + +
590B ALA* 3.3 0.8 - - - -
591B SER* 2.8 29.1 + - - +
593B HIS* 3.1 18.7 + - - +
594B SER 4.1 11.7 - - - -
595B ASN* 3.4 23.5 - - + +
600B PRO* 1.3 69.4 - - - +
602B GLY* 1.3 57.8 + - - +
709B ASN 3.2 15.9 - - - +
710B PHE* 2.8 46.1 + - + -
711B PHE* 5.4 1.0 - - - +
712B ASP* 5.7 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 602 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B VAL* 3.9 2.7 - - - -
588B TYR* 4.3 5.6 - - - -
589B LEU 3.2 12.6 - - - -
590B ALA* 3.3 9.0 - - - -
600B PRO 3.1 3.0 + - - -
601B ARG* 1.3 76.1 - - - +
603B TYR* 1.3 63.6 + - - -
708B TYR* 2.9 37.7 + - - +
710B PHE* 3.3 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 603 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU* 3.4 30.4 - - + +
483B GLY 2.5 32.3 + - - -
485B ILE* 5.2 1.8 - - + -
530B LEU* 4.5 23.0 - - + +
532B VAL* 4.0 10.9 - - + +
588B TYR* 3.0 13.4 - - - +
589B LEU* 2.8 18.1 + - - +
602B GLY* 1.3 79.5 - - - -
604B ARG* 1.3 63.1 + - - +
605B ILE* 4.5 4.7 - - - +
705B LEU* 3.6 25.8 - - + -
706B ARG 3.4 13.2 - - - -
707B PRO* 3.4 21.0 - - + +
710B PHE* 3.5 35.2 - + - -
711B PHE* 3.4 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 604 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A LEU 5.0 1.8 + - - -
699A ASN* 5.1 0.2 + - - -
585B ARG* 2.6 29.1 + - - +
586B TYR* 3.4 49.2 + - + +
587B LEU 3.4 14.3 - - - +
588B TYR* 3.3 12.3 - - + +
602B GLY 4.2 0.6 - - - -
603B TYR* 1.3 73.4 - - - +
605B ILE* 1.3 69.5 + - - +
606B GLN* 4.0 26.3 - - - +
704B PHE 3.3 5.2 - - - +
705B LEU* 3.4 4.3 - - - +
706B ARG* 2.6 79.9 + - - +
707B PRO 5.5 0.2 - - - -
708B TYR* 4.5 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 605 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B VAL* 5.7 0.7 - - + -
530B LEU* 4.8 7.2 - - + -
587B LEU* 2.9 28.4 + - + +
588B TYR* 5.2 2.0 - - - -
589B LEU* 4.6 17.9 - - + -
603B TYR 4.5 6.7 - - - +
604B ARG* 1.3 79.0 + - - +
606B GLN* 1.3 61.6 + - - +
607B MET* 4.1 24.7 + - + +
632B LEU* 4.6 19.4 - - + +
634B VAL* 5.7 0.7 - - + -
676B ALA* 3.7 30.5 - - + -
678B VAL* 4.5 15.7 - - + -
703B PHE* 5.0 3.1 - - + -
704B PHE 3.4 6.5 - - - +
705B LEU* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 606 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A PHE* 3.9 38.9 - - + -
682A PHE* 6.2 1.2 - - - +
698A GLY 3.3 14.1 + - - +
699A ASN* 4.9 2.2 + - - -
604B ARG* 4.0 28.3 - - - +
605B ILE* 1.3 75.1 - - - +
607B MET* 1.3 63.8 - - - +
608B LEU* 4.7 4.9 - - + -
703B PHE* 3.1 4.0 - - - +
704B PHE* 2.6 55.7 + - + -
706B ARG* 2.9 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 607 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A PHE* 3.7 17.3 - - - -
583B THR* 4.3 17.9 - - + +
587B LEU* 5.9 2.0 - - + -
605B ILE* 4.1 15.0 + - + +
606B GLN* 1.3 74.3 - - - +
608B LEU* 1.3 75.3 + - - +
609B SER* 3.8 11.4 - - - +
631B GLN* 3.8 46.7 - - - +
632B LEU* 4.0 23.1 - - + -
678B VAL* 3.9 20.2 - - + -
679B THR 5.2 1.6 - - - +
702B GLY 3.7 6.3 - - - +
703B PHE* 4.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 608 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A PHE* 4.3 17.9 - - + -
698A GLY 6.2 0.2 - - - +
488B ARG* 2.8 47.6 - - - +
606B GLN* 4.7 4.0 - - + +
607B MET* 1.3 90.0 - - - +
609B SER* 1.3 58.4 + - - +
610B PHE* 4.5 11.1 - - + -
700B GLY 5.0 1.1 - - - +
701B VAL* 3.0 30.5 - - + +
702B GLY 3.0 19.4 + - - +
703B PHE* 4.1 9.4 - - - +
704B PHE* 4.0 26.9 - - + -
----------------------------------------------------------
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