Contacts of the strand formed by residues 2 - 10 (chain B) in PDB entry 3F7F
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 2 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 1.3 78.2 - - + +
3B CYS* 1.3 62.4 + - - +
4B LEU 3.6 0.4 - - - -
380B GLU* 3.2 7.6 - - + -
381B SER* 3.8 24.2 - - - +
382B VAL* 4.0 15.3 - - + +
487B ASN* 3.6 6.2 + - - -
492B ASN* 3.3 7.1 - - - +
495B TYR* 4.8 4.0 - - + +
496B ASN* 3.2 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 3 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 3.8 8.3 + - - -
2B ALA* 1.3 75.0 - - - +
4B LEU* 1.3 74.4 + - + +
342B LEU* 4.6 4.5 - - + -
343B ASN* 3.1 35.4 - - - +
379B ILE* 3.8 23.8 - - + -
380B GLU 3.0 6.1 + - - -
486B LEU* 3.8 5.7 - - + +
487B ASN* 2.9 31.8 + - - +
492B ASN* 3.8 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 4 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B CYS* 1.3 95.4 + - + +
5B SER* 1.3 64.8 + - - +
340B LEU* 5.0 2.7 - - + -
342B LEU* 4.5 6.5 - - + -
363B LEU* 4.3 6.1 - - + -
365B ILE* 3.9 20.2 - - + -
379B ILE* 4.2 11.9 - - + +
380B GLU 4.3 3.4 - - - +
381B SER* 3.5 16.2 - - - -
382B VAL* 3.0 29.5 + - - +
471B ILE* 3.8 29.4 - - + -
484B TYR* 4.1 22.9 - - + +
485B LYS 3.3 9.6 - - - +
486B LEU* 4.2 9.9 - - + +
487B ASN* 3.5 3.6 + - - -
695B TYR* 4.4 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 1.3 74.4 - - - +
6B ARG* 1.3 61.5 + - - +
7B ILE* 4.5 1.3 - - - +
382B VAL* 4.3 4.9 - - - -
484B TYR* 3.2 10.4 - - - -
485B LYS* 2.8 44.2 + - - +
487B ASN* 2.6 21.3 + - - -
495B TYR* 3.6 27.6 - - - -
621B GLN* 3.1 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B SER* 1.3 74.5 - - - +
7B ILE* 1.3 71.5 + - - +
8B ASP* 2.8 26.8 + - - +
361B SER* 4.2 13.3 + - - +
382B VAL* 3.8 15.6 + - - +
383B ASN 2.8 35.7 + - - -
384B LYS* 4.0 21.8 + - - +
385B SER* 3.5 23.1 - - - +
386B LEU 4.4 0.9 + - - -
388B ASP* 5.3 2.4 + - - -
454B LYS* 5.0 1.6 - - - +
458B ASN* 3.1 43.9 + - - +
482B SER* 3.5 11.2 + - - +
483B LEU 3.7 2.9 - - - +
484B TYR* 3.5 28.2 + - + -
495B TYR* 5.3 0.6 + - - -
621B GLN* 4.3 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B SER* 4.5 2.5 - - - +
6B ARG* 1.3 82.3 - - - +
8B ASP* 1.3 61.9 + - - +
9B ALA 3.6 0.5 + - - -
385B SER* 5.1 0.2 - - - -
482B SER* 3.6 0.3 - - - -
483B LEU* 2.8 48.0 + - + +
485B LYS* 4.0 21.8 - - + -
614B ILE* 4.1 17.9 - - + +
617B GLU* 3.4 31.9 - - + +
618B SER* 4.0 27.8 - - - +
621B GLN* 3.9 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ARG* 2.8 25.5 + - - +
7B ILE* 1.3 73.4 - - - +
9B ALA* 1.3 61.4 + - - +
10B ASN 4.1 1.4 + - - -
13B GLN* 5.4 0.9 - - - +
385B SER* 3.5 23.1 + - - -
388B ASP* 3.6 2.6 - - - +
454B LYS* 3.1 29.7 + - - +
458B ASN* 3.8 11.9 - - - +
481B HIS 3.9 1.6 - - - +
482B SER* 2.5 29.3 + - - +
613B ILE* 4.7 1.2 - - - +
617B GLU* 3.7 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE 3.6 0.8 + - - +
8B ASP* 1.3 75.1 - - - +
10B ASN* 1.3 60.0 + - - +
11B LEU* 3.7 3.7 + - + -
479B TYR 3.6 1.0 - - - +
480B ASN* 3.4 3.0 - - - -
481B HIS* 2.7 48.8 + - + +
483B LEU 5.5 0.2 - - - +
610B PHE* 4.3 14.4 - - + -
613B ILE* 4.5 15.9 - - + -
614B ILE* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASP 4.1 1.4 + - - -
9B ALA* 1.3 74.0 - - - +
11B LEU* 1.3 51.9 + - - +
12B LEU* 2.7 32.7 + - - +
13B GLN* 2.7 41.3 + - + +
415B TYR 5.4 6.3 - - - +
416B GLY* 6.1 1.3 - - - -
418B GLN* 3.0 27.0 + - - +
419B ILE* 4.4 13.8 - - + +
479B TYR* 3.2 7.0 - - - +
480B ASN* 2.7 27.5 + - - +
613B ILE* 4.6 8.9 - - - +
----------------------------------------------------------
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