Contacts of the strand formed by residues 31 - 38 (chain A) in PDB entry 3CFV
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 TYR 31 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 2.9 32.9 + + - -
27A THR* 2.9 34.4 + - + +
28A PRO* 4.2 9.7 - - - +
29A PHE 3.6 0.2 - - - -
30A LEU* 1.3 96.5 - - + +
32A ASP* 1.3 64.1 + - - +
33A LEU 3.7 11.7 - - - +
34A VAL* 3.4 28.4 - - + +
367A PHE* 3.5 25.1 - + - -
368A ILE 4.7 0.3 + - - -
369A HIS* 2.7 27.0 + + - -
401A TRP* 3.6 19.1 - + - -
402A GLN 3.3 22.2 - - - +
403A MSE 4.1 0.4 - - - -
404A ALA* 3.5 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TYR* 1.3 74.4 - - - +
33A LEU* 1.3 59.8 + - - +
88A ASP* 5.1 14.4 - - - +
402A GLN* 2.8 26.4 + - - +
403A MSE 3.8 3.0 - - - +
404A ALA* 3.6 16.7 - - - +
405A GLU* 2.9 32.3 + - - +
406A ASN* 5.7 0.2 + - - -
408A TYR* 4.9 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TYR* 3.3 1.0 - - - +
32A ASP* 1.3 82.6 - - - +
34A VAL* 1.3 74.1 + - - +
35A MSE 3.5 44.9 - - + -
85A ILE* 4.1 15.3 - - + -
86A PRO* 4.6 14.8 - - + +
111A THR* 5.7 3.1 - - - +
388A VAL* 4.6 11.2 - - + -
400A ILE* 4.1 11.7 - - + +
401A TRP* 3.1 3.6 - - - -
402A GLN* 2.8 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 4.4 16.4 - - + -
27A THR* 4.3 18.2 - - + +
31A TYR* 3.4 41.3 - - + -
33A LEU* 1.3 82.4 - - - +
35A MSE 1.3 65.9 + - - +
36A THR* 4.3 4.7 - - + -
111A THR* 4.0 10.2 + - - -
369A HIS* 5.4 0.7 - - + -
399A GLN* 6.3 1.3 - - + -
400A ILE 3.7 2.5 - - - -
401A TRP* 3.9 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.5 30.1 - - + -
34A VAL* 1.3 79.5 - - - +
36A THR* 1.3 62.9 + - - +
83A VAL* 6.4 0.2 - - - -
84A HIS 3.9 17.5 - - - +
85A ILE* 3.8 19.7 - - + -
86A PRO* 4.1 7.2 - - - -
111A THR* 3.5 28.7 - - - +
112A GLY* 4.0 5.2 - - - -
398A MSE 3.8 0.3 - - - +
399A GLN* 3.1 6.9 - - - +
400A ILE* 2.8 85.5 + - + +
401A TRP* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 5.0 9.4 + - - +
23A TRP* 5.2 6.1 - - + -
34A VAL* 5.4 3.4 - - + -
35A MSE 1.3 78.2 - - - +
37A HIS* 1.3 64.5 + - - +
397A ILE* 5.1 7.9 - - + -
398A MSE 3.4 3.8 - - - -
399A GLN* 3.1 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A THR* 1.3 77.4 - - - +
38A ALA* 1.3 86.0 + - - +
39A LEU* 3.8 10.8 + - + +
114A ILE* 3.8 32.8 - - + +
396A ASN 3.7 0.7 - - - +
397A ILE* 3.8 5.9 - - - -
398A MSE 2.9 68.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A HIS* 1.3 92.7 + - - +
39A LEU* 1.3 66.0 + - - +
40A GLN 4.1 0.2 + - - -
396A ASN* 3.7 9.2 - - + +
397A ILE* 4.2 15.5 - - + -
----------------------------------------------------------
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