Contacts of the strand formed by residues 713 - 718 (chain N) in PDB entry 3EQL
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 ILE 713 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032M PHE* 4.7 6.7 - - + -
1036M GLU* 4.0 22.7 - - + +
1039M ALA* 3.9 22.7 - - + -
1040M LEU* 4.0 22.4 - - + -
1043M TYR* 3.1 23.3 + - + -
701N LEU* 4.4 22.7 - - + -
702N LEU 3.3 9.9 - - - +
703N ASN* 3.5 29.8 - - + +
707N THR* 4.3 1.1 - - - +
710N ARG 3.3 7.7 + - - +
711N LEU 2.7 2.9 + - - -
712N GLY* 1.3 89.7 - - - +
714N GLN* 1.3 60.7 + - - +
736N PHE* 4.3 0.2 - - - -
748N HIS* 6.2 0.9 - - + +
763N MET* 4.4 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 714 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043M TYR* 4.1 9.4 - - - +
701N LEU* 3.5 3.2 - - - -
702N LEU 2.9 29.4 + - - +
711N LEU* 3.4 26.7 + - + +
713N ILE* 1.3 75.7 - - - +
715N ALA* 1.3 61.3 + - - +
716N PHE* 3.8 12.3 - - + -
732N VAL* 3.1 17.1 - - - +
735N ALA* 3.1 33.9 - - - +
736N PHE* 3.8 20.2 - - + -
763N MET* 3.8 6.3 - - - +
765N SER* 3.1 33.1 - - - +
768N ASN* 4.9 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 715 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699N VAL* 4.7 7.6 - - + -
700N VAL 3.3 11.4 - - - +
701N LEU* 4.3 14.4 - - + +
714N GLN* 1.3 72.6 - - - +
716N PHE* 1.3 71.4 + - - +
759N ALA 3.5 21.3 - - - +
763N MET* 2.9 21.4 + - + +
764N LEU* 3.1 8.2 - - + +
765N SER 2.8 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 716 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639N LEU 3.4 3.4 - - - -
640N HIS 3.4 6.3 - - - +
641N GLN 3.3 28.9 - - - +
642N CYS* 3.8 9.6 - - + -
699N VAL* 3.0 22.3 - - - +
700N VAL* 3.0 20.4 + - - +
702N LEU* 3.3 47.6 - - + -
714N GLN* 3.8 14.6 - - + -
715N ALA* 1.3 82.2 - - - +
717N GLN* 1.3 60.4 + - - +
718N PRO* 3.4 3.2 - - - +
728N LEU* 4.3 5.2 - - + -
729N HIS* 5.5 1.8 - - + -
732N VAL* 4.1 20.0 - - + -
736N PHE* 3.8 22.2 - + - -
764N LEU* 3.9 2.5 - - - -
765N SER* 3.2 32.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 717 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640N HIS* 3.2 42.3 + - - +
641N GLN* 3.1 32.2 - - + +
642N CYS 3.3 4.0 + - - -
695N ILE 5.6 0.4 - - - +
696N HIS 4.4 13.8 - - - +
697N GLY* 4.9 5.1 - - - -
698N LYS 3.7 9.4 - - - +
699N VAL* 3.5 18.0 - - + +
716N PHE* 1.3 72.9 - - - +
718N PRO* 1.3 68.1 - - - +
719N VAL* 5.1 0.2 - - - +
760N ARG* 4.7 7.1 - - - +
764N LEU* 6.0 0.8 - - - +
3O GLU* 4.0 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 718 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642N CYS* 3.6 9.0 - - - +
644N LEU* 3.5 24.9 - - + -
653N PHE* 5.0 4.0 - - + -
695N ILE* 3.8 32.3 - - + +
698N LYS 3.4 19.3 - - - +
699N VAL* 3.9 2.5 - - - -
700N VAL* 3.6 37.0 - - + -
716N PHE 3.4 6.3 - - - +
717N GLN* 1.3 85.2 - - + +
719N VAL* 1.3 62.8 + - - +
720N LEU* 3.7 3.9 + - - +
----------------------------------------------------------
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