Contacts of the strand formed by residues 70 - 75 (chain D) in PDB entry 1VQM
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 GLY 70 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23460 C 4.7 3.6 - - - -
25D MET 3.5 14.8 - - - -
26D GLY* 4.8 0.2 - - - -
27D ILE* 4.4 0.9 - - - -
35D ALA 4.5 13.3 + - - +
51D ARG* 3.4 7.8 - - - +
52D THR* 2.8 37.8 + - - -
68D PRO* 5.6 0.2 - - - +
69D ILE* 1.3 82.8 + - - +
71D ALA* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D HIS* 3.1 7.2 - - - +
25D MET* 3.0 31.8 + - + +
35D ALA 4.9 4.3 - - - +
37D ALA* 5.8 1.1 - - + -
38D GLU* 4.1 26.9 - - + +
41D LEU* 3.8 10.1 - - + +
49D PRO* 4.4 8.3 - - + -
50D VAL 2.9 17.5 - - - +
51D ARG* 4.6 0.4 - - - -
52D THR* 3.6 3.7 + - - -
70D GLY* 1.3 76.1 - - - +
72D LYS* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23470 C 3.2 31.9 + - - +
23480 C 2.6 27.9 + - - -
30419 C 4.0 25.2 - - - +
22D VAL* 4.1 13.0 - - + -
23D VAL 3.0 7.4 - - - +
24D HIS* 3.3 22.2 - - + -
49D PRO* 3.3 1.6 - - - +
50D VAL* 2.8 45.9 + - + +
51D ARG 5.9 1.1 - - - +
52D THR* 4.5 3.8 + - - +
71D ALA* 1.3 72.3 - - - +
73D VAL* 1.3 66.5 + - - +
74D THR* 4.6 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30419 C 3.6 2.9 - - - -
21D VAL 3.2 4.9 - - - +
22D VAL* 4.3 0.7 - - - -
23D VAL* 2.7 52.0 + - + +
41D LEU* 4.1 13.5 - - + -
45D THR* 3.8 11.9 - - + +
47D GLN* 3.3 43.5 - - + +
48D MET 3.7 4.9 - - - +
49D PRO* 3.5 23.1 - - + -
72D LYS* 1.3 80.2 - - - +
74D THR* 1.3 62.4 + - - +
75D LEU* 3.7 7.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23480 C 5.5 1.3 - - - +
30419 C 2.9 44.2 + - - +
30429 C 3.2 31.3 + - + +
20D LYS* 5.1 4.3 - - + +
21D VAL 3.5 4.0 - - - -
22D VAL* 3.7 29.4 - - + +
47D GLN* 2.4 27.0 - - - +
72D LYS* 4.6 8.3 - - - +
73D VAL* 1.3 73.7 - - - +
75D LEU* 1.3 56.0 + - - +
76D ARG* 4.3 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30429 C 4.7 0.4 - - - -
20D LYS* 3.1 7.1 - - - -
21D VAL* 2.7 46.1 + - + +
23D VAL* 4.8 2.0 - - + -
45D THR* 4.0 26.5 - - + +
47D GLN* 3.5 34.8 - - + +
73D VAL* 4.1 9.6 - - + +
74D THR* 1.3 74.1 - - - +
76D ARG* 1.3 59.6 + - - +
79D MET* 3.2 31.4 - - + +
80D ALA* 3.7 18.2 - - + +
83D PHE* 3.7 28.0 - - + -
----------------------------------------------------------
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