Contacts of the strand formed by residues 43 - 51 (chain A) in PDB entry 1VEP
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 PHE 43 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA 3.5 6.1 - - - +
14A TYR 3.3 35.4 - - - -
15A LEU* 3.7 24.2 - - + -
38A ALA* 3.1 41.6 + - + +
39A LYS* 3.5 20.8 - - - +
41A ASN* 3.6 2.0 - - + -
42A GLY* 1.3 75.8 - - - +
44A TYR* 1.3 63.5 + - - +
45A ALA 4.6 3.6 - - - +
80A MET* 3.8 11.9 - - + +
395A LEU* 4.1 13.2 - - + -
401A VAL* 4.4 2.0 - - + -
408A MET* 4.0 22.0 - - + -
411A PHE* 3.2 49.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 3.5 51.2 - - + -
13A ALA 2.7 17.2 + - - +
14A TYR* 3.9 14.1 - + + -
42A GLY 3.4 3.6 + - - +
43A PHE* 1.3 73.2 - - - +
45A ALA* 1.3 61.9 + - + +
80A MET* 3.8 6.4 - - - +
81A LYS* 3.2 47.9 + - + +
161A ALA* 4.0 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA 3.8 2.2 + - - +
14A TYR* 3.3 18.9 - - + -
15A LEU* 2.9 25.5 + - - +
43A PHE* 3.5 1.7 - - - +
44A TYR* 1.3 85.9 + - + +
46A ILE* 1.3 61.9 + - - +
47A MET 4.1 0.2 - - - -
80A MET* 3.8 10.9 - - - +
81A LYS* 3.0 30.7 - - + +
82A MET* 3.8 8.3 - - - +
83A ILE* 4.5 7.2 - - + -
161A ALA* 4.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.2 20.6 - - + +
17A ALA* 3.6 31.4 - - + -
31A PHE* 4.1 17.7 - - + -
35A LEU* 4.0 30.1 - - + -
45A ALA* 1.3 73.6 - - - +
47A MET* 1.3 60.3 + - - +
48A VAL* 3.9 1.2 + - - +
71A PHE* 4.2 15.7 - - + -
75A VAL* 4.2 9.6 - - + -
80A MET* 4.2 2.9 - - + +
81A LYS 3.0 16.3 + - - +
82A MET* 3.2 11.3 - - + +
83A ILE* 3.0 21.1 + - - -
398A TYR* 4.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 4.4 5.8 - - + +
15A LEU 2.8 9.3 + - - +
16A MET* 3.0 20.2 - - - +
17A ALA* 2.9 26.9 + - - +
45A ALA 4.1 1.4 + - - -
46A ILE* 1.3 72.3 - - - +
48A VAL* 1.3 60.5 + - - +
83A ILE* 3.2 46.7 - - + +
85A ILE* 3.5 31.0 - - + -
162A LYS* 5.8 1.8 - - - +
164A GLU* 4.3 12.6 - - + +
287A LYS* 4.4 1.6 - - - -
328A ASN* 4.3 9.4 - - - +
367A GLU* 4.0 14.1 - - - +
394A THR* 3.1 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A MET* 3.7 6.1 - - - -
17A ALA* 3.9 12.8 - - + -
18A PRO 5.3 3.4 - - - +
46A ILE 4.6 3.4 - - - +
47A MET* 1.3 76.0 - - - +
49A ASP* 1.3 72.4 + - - +
50A PHE* 3.7 24.7 + - + -
67A TYR* 5.6 3.1 - - + +
71A PHE* 3.6 46.2 - - + -
82A MET* 4.2 6.5 - - + -
83A ILE 3.0 9.0 + - - +
84A PRO* 3.6 0.9 - - - +
85A ILE* 2.8 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A MET* 3.6 5.0 - - - +
18A PRO 5.2 4.8 + - - +
19A LEU* 4.3 3.5 - - - +
48A VAL* 1.3 82.3 - - - +
50A PHE* 1.3 69.9 + - - +
51A TRP* 3.4 41.6 + - + +
67A TYR* 5.3 3.3 - - - -
85A ILE* 3.7 7.3 - - - +
87A SER* 2.7 22.0 + - - +
397A ARG* 4.8 0.3 + - - -
2B GLC 2.4 51.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 3.7 17.3 - - + -
49A ASP* 1.3 77.7 - - - +
51A TRP* 1.3 61.1 + - - +
55A MET* 3.0 32.7 - - + +
67A TYR* 4.1 24.0 - + - -
68A ALA* 3.7 35.0 - - + -
71A PHE* 4.0 12.1 - + + -
82A MET* 3.3 35.9 - - + -
84A PRO* 3.6 24.0 - - + -
85A ILE 3.0 11.4 + - - +
86A ILE* 5.2 1.3 - - - -
87A SER* 3.1 19.4 + - - -
149A PHE* 3.8 18.4 - + + -
153A MET* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.0 19.9 + - + -
21A LYS* 5.0 5.6 - - + -
49A ASP* 3.4 42.5 + - + +
50A PHE* 1.3 70.2 - - - +
52A TRP* 1.3 65.1 + - - +
53A GLY 4.0 0.4 - - - +
54A ASP* 3.0 31.7 + - - +
55A MET* 3.0 18.5 + - - +
87A SER* 3.5 17.0 - - - -
89A HIS* 3.4 44.6 - + - +
91A CYS* 3.2 42.2 - - + -
101A VAL* 3.6 29.5 - - + +
2B GLC 3.3 22.4 - - - -
----------------------------------------------------------
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