Contacts of the strand formed by residues 55 - 62 (chain S) in PDB entry 2VGL
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 55 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434M ARG* 5.7 0.7 + - - -
3S ARG* 3.8 29.2 - - + -
4S PHE* 5.8 1.1 - + - -
21S MET* 4.1 31.9 - - + -
23S PHE* 5.1 7.9 - + - -
31S LEU* 6.5 0.4 - - + -
51S GLU* 3.6 4.7 - - - +
52S PHE* 2.7 30.4 + + - +
53S ARG* 4.5 8.0 - - + +
54S ASN* 1.3 114.9 - - - +
56S LYS* 1.3 68.0 + - - +
70S CYS* 3.5 24.9 - - - -
71S VAL 3.4 12.6 - - - +
72S ASP* 3.9 15.5 - - - -
73S VAL* 4.2 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 56 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49S PHE* 5.5 3.8 - - + -
50S VAL 3.3 14.4 - - - +
51S GLU* 4.0 10.8 - - + -
52S PHE* 4.0 2.2 - - - +
55S PHE* 1.3 81.1 - - - +
57S ILE* 1.3 64.9 + - - +
58S ILE* 4.7 2.5 - - + -
70S CYS* 3.1 6.1 - - - -
71S VAL* 2.8 39.9 + - + +
72S ASP 3.2 19.1 - - - +
73S VAL* 2.7 34.7 + - + +
75S ASP 2.8 21.6 + - - -
77S ASN* 3.0 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 57 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4S PHE* 5.1 1.1 - - + -
35S VAL* 3.7 27.1 - - + -
38S VAL* 5.3 2.2 - - + -
39S VAL* 4.6 7.9 - - + -
48S ASN 3.5 1.0 - - - +
49S PHE* 3.3 5.2 - - - -
50S VAL* 2.8 45.2 + - + +
52S PHE* 3.4 41.7 - - + -
56S LYS* 1.3 81.0 - - - +
58S ILE* 1.3 78.7 + - - +
59S TYR* 4.2 11.9 - - + -
68S CYS* 4.1 15.9 - - + -
69S ILE 3.3 6.5 - - - +
70S CYS* 4.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48S ASN 3.1 7.4 - - - +
49S PHE* 4.3 7.4 - - + -
56S LYS* 4.7 2.7 - - + -
57S ILE* 1.3 81.3 - - - +
59S TYR* 1.3 65.3 + - - +
68S CYS* 3.4 1.4 - - - -
69S ILE* 3.0 32.5 + - + +
71S VAL* 4.6 17.5 - - + -
77S ASN* 3.2 39.0 - - + +
80S TYR* 3.9 20.0 - - + -
81S LEU* 3.5 45.5 - - + +
84S ILE* 3.7 8.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 59 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39S VAL* 3.8 26.2 - - + -
42S ARG* 2.9 50.3 + - + +
43S ASP 5.0 1.7 + - - -
46S HIS* 4.4 1.9 - - - +
47S THR 3.1 12.1 + - - -
48S ASN* 3.0 56.1 + - - +
50S VAL* 4.6 5.6 - - + -
57S ILE* 4.2 8.5 - - + -
58S ILE* 1.3 76.6 - - - +
60S ARG* 1.3 71.1 + - - +
61S ARG* 5.3 2.0 - - + -
66S TYR* 4.2 20.6 - + - -
67S PHE 3.1 15.3 - - - +
68S CYS* 4.0 16.4 - - - -
81S LEU* 3.9 4.5 - - - +
84S ILE* 4.2 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A VAL* 4.3 13.0 - - - +
301A GLN* 4.0 18.1 - - - +
304A ASN* 4.0 15.0 - - - +
342A GLU* 5.0 4.0 + - - -
344A ASN* 4.8 1.8 - - - +
48S ASN* 3.9 26.3 + - - +
59S TYR* 1.3 84.0 - - - +
61S ARG* 1.3 79.8 + - - +
62S TYR* 3.7 34.0 + - + +
65S LEU 3.7 0.2 - - - +
66S TYR* 3.4 1.1 - - - -
67S PHE* 2.9 33.4 + - - +
81S LEU* 4.2 24.2 + - + +
82S GLU* 3.6 22.2 + - - -
84S ILE* 4.7 6.4 - - + +
85S HIS* 5.1 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S ARG* 3.0 26.9 - - - +
44S ALA* 6.1 2.6 - - - +
59S TYR* 4.9 2.6 - - + -
60S ARG* 1.3 87.6 - - - +
62S TYR* 1.3 68.3 + - - +
63S ALA* 2.9 37.3 + - - +
65S LEU 3.0 11.2 - - - +
66S TYR* 3.4 43.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 62 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B SER 3.7 28.0 - - - -
6B TYR* 3.7 25.1 - + + +
7B PHE* 3.9 14.8 - - + +
60S ARG* 3.7 36.8 - - + -
61S ARG* 1.3 76.9 - - - +
63S ALA* 1.3 71.9 + - - +
64S GLY 2.9 1.0 + - - -
65S LEU* 2.7 27.2 + - - +
67S PHE* 3.7 20.4 - + + -
81S LEU 5.4 0.2 + - - -
84S ILE* 4.1 10.5 - - + +
85S HIS* 2.7 42.9 + + - +
88S VAL* 4.1 24.7 - - + -
----------------------------------------------------------
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