Contacts of the strand formed by residues 2 - 10 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 1.3 77.9 - - + +
3C CYS* 1.3 60.1 + - - +
4C LEU 3.6 0.7 - - - -
380C GLU* 3.2 8.1 - - + -
381C SER* 3.8 24.7 - - - +
382C VAL* 4.0 14.8 - - + +
487C ASN* 3.5 5.4 + - - -
492C ASN* 3.3 7.4 - - - +
495C TYR* 4.8 3.3 - - + +
496C ASN* 3.2 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 3 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET 4.7 8.1 - - - -
2C ALA* 1.3 75.3 - - - +
4C LEU* 1.3 71.6 + - + +
342C LEU* 4.6 4.9 - - + -
343C ASN* 3.0 35.4 - - - +
379C ILE* 3.8 24.9 - - + -
380C GLU 3.0 6.7 + - - -
486C LEU* 3.7 7.8 - - + +
487C ASN* 2.8 32.1 + - - +
492C ASN* 3.8 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 4 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C CYS* 1.3 96.4 + - + +
5C SER* 1.3 62.5 + - - +
340C LEU* 5.0 2.7 - - + -
342C LEU* 4.5 6.3 - - + -
363C LEU* 4.4 5.2 - - + -
365C ILE* 3.9 20.4 - - + -
379C ILE* 4.2 10.8 - - + +
380C GLU 4.4 3.4 - - - +
381C SER* 3.5 16.5 - - - -
382C VAL* 3.0 28.9 + - - +
471C ILE* 3.8 29.2 - - + -
484C TYR* 4.0 22.9 - - + +
485C LYS 3.2 9.4 - - - +
486C LEU* 4.2 10.5 - - + +
487C ASN* 3.5 5.4 + - - -
695C TYR* 4.3 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 5 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 1.3 73.9 - - - +
6C ARG* 1.3 60.1 + - - +
7C ILE* 4.0 1.3 + - - +
382C VAL* 4.4 5.8 - - - -
483C LEU 3.7 0.2 - - - +
484C TYR* 3.2 9.7 - - - -
485C LYS* 2.7 44.1 + - - +
487C ASN* 2.7 21.8 + - - -
495C TYR* 3.6 18.6 - - - -
621C GLN* 3.1 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 6 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C SER* 1.3 74.3 - - - +
7C ILE* 1.3 71.3 + - - +
8C ASP* 2.8 26.4 + - - +
361C SER* 4.2 13.1 + - - +
382C VAL* 3.8 15.2 + - - +
383C ASN 2.8 35.7 + - - -
384C LYS* 4.0 21.1 + - - +
385C SER* 3.5 23.6 - - - +
386C LEU 4.4 0.7 + - - -
388C ASP* 5.4 1.8 + - - -
454C LYS* 5.0 1.2 - - - +
458C ASN* 3.0 44.3 + - - +
482C SER* 3.5 12.0 + - - -
483C LEU 3.7 2.9 - - - +
484C TYR* 3.5 28.5 + - + -
495C TYR* 5.3 0.7 + - - -
621C GLN* 4.3 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 7 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C SER* 4.5 2.7 - - - +
6C ARG* 1.3 81.6 - - - +
8C ASP* 1.3 62.6 + - - +
9C ALA 3.6 0.9 + - - -
385C SER* 5.2 0.4 - - - -
483C LEU* 2.8 49.2 + - + +
485C LYS* 4.0 19.7 - - + -
614C ILE* 4.0 18.6 - - + +
617C GLU* 3.4 30.7 - - + +
618C SER* 4.0 28.3 - - - +
621C GLN* 3.9 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 8 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ARG* 2.8 24.2 + - - +
7C ILE* 1.3 73.8 - - - +
9C ALA* 1.3 59.3 + - - +
10C ASN 4.2 0.9 + - - -
13C GLN* 5.3 1.2 - - - +
385C SER* 3.6 21.8 - - - -
388C ASP* 3.7 2.4 - - - +
454C LYS* 3.1 29.0 + - - +
458C ASN* 3.8 11.9 - - - +
481C HIS 3.9 1.6 - - - +
482C SER* 2.5 29.0 + - - +
613C ILE* 4.6 0.9 - - - +
617C GLU* 3.7 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 9 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE 3.6 1.0 + - - +
8C ASP* 1.3 74.1 - - - +
10C ASN* 1.3 60.0 + - - +
11C LEU* 3.7 3.3 + - + -
479C TYR 3.6 1.0 - - - +
480C ASN* 3.3 3.7 - - - -
481C HIS* 2.7 48.1 + - + +
482C SER* 5.4 0.4 - - - -
610C PHE* 4.3 15.3 - - + -
613C ILE* 4.4 15.0 - - + -
614C ILE* 3.6 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 10 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ASP 4.2 2.2 + - - -
9C ALA* 1.3 73.4 - - - +
11C LEU* 1.3 52.4 + - - +
12C LEU* 2.7 32.6 + - - +
13C GLN* 2.7 42.1 + - + +
415C TYR 5.4 6.1 - - - +
416C GLY* 6.2 0.9 - - - -
418C GLN* 3.0 28.3 + - - +
419C ILE* 4.5 13.6 - - + +
479C TYR* 3.2 7.0 - - - +
480C ASN* 2.7 27.4 + - - +
613C ILE* 4.6 8.1 - - - +
----------------------------------------------------------
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