Contacts of the strand formed by residues 80 - 86 (chain H) in PDB entry 1V7M
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 SER 80 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H SER* 6.2 0.4 - - - -
22H CYS 3.0 13.8 + - - -
23H ALA* 4.2 7.1 - - - +
29H PHE* 3.0 17.0 - - - -
74H ARG* 3.2 1.0 - - - -
75H ASP 2.9 28.3 + - - -
78H LYS* 2.9 24.8 + - - +
79H SER* 1.3 77.3 + - - +
81H VAL* 1.3 60.1 + - - +
82H TYR* 3.7 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H SER 3.7 0.5 - - - -
22H CYS* 2.9 50.3 + - + +
29H PHE* 4.2 8.5 - - + -
34H MET* 3.9 30.3 - - + -
36H TRP* 4.0 21.4 - - + +
51H ILE* 3.7 26.5 - - + -
72H VAL* 4.6 2.0 - - + -
73H SER 3.1 18.8 - - - +
74H ARG* 4.1 2.9 - - + +
80H SER* 1.3 76.1 - - - +
82H TYR* 1.3 67.7 + - - +
98H CYS* 4.3 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H LYS* 4.1 29.8 - - - +
20H LEU 3.4 7.6 - - - +
21H SER* 3.5 26.0 - - - -
36H TRP* 3.4 12.1 + - - -
71H THR 4.4 0.2 - - - -
72H VAL* 3.2 6.6 - - - +
73H SER* 2.6 56.8 + - - +
74H ARG* 4.3 2.7 - - - -
75H ASP* 3.8 31.7 + - + +
78H LYS* 4.4 11.3 - - - +
80H SER* 3.7 27.4 + - - -
81H VAL* 1.3 83.9 - - - +
83H LEU* 1.3 60.5 + - - +
84H GLN* 4.0 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H MET 3.7 0.5 - - - +
19H LYS* 3.5 1.0 - - - -
20H LEU* 2.9 40.4 + - + +
36H TRP* 3.9 33.1 - - + +
48H VAL* 4.9 10.5 - - + -
49H ALA* 5.0 4.7 - - + -
62H TYR* 5.5 0.4 - - + -
70H PHE* 3.8 31.6 - - + -
71H THR 3.4 15.9 - - - +
72H VAL* 4.6 5.6 - - + -
82H TYR* 1.3 75.6 - - - +
84H GLN* 1.3 62.7 + - - +
85H MET* 3.4 37.0 + - + +
96H TYR* 4.3 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H SER* 4.6 4.4 + - - -
18H MET 3.9 6.4 + - - +
19H LYS* 3.5 36.8 + - - +
69H ARG 3.7 1.7 - - - +
70H PHE* 3.2 3.0 - - - -
71H THR* 2.6 57.3 + - + +
82H TYR* 4.0 2.0 - - + +
83H LEU* 1.3 72.1 - - - +
85H MET* 1.3 65.7 + - - +
86H ASN* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H SER* 3.2 2.1 - - - -
18H MET* 2.9 74.7 + - + +
20H LEU* 4.2 8.3 - - + -
70H PHE* 3.5 35.7 - - + -
83H LEU* 3.5 33.4 - - + +
84H GLN* 1.3 72.6 + - - +
86H ASN* 1.4 68.7 + - - +
88H LEU* 3.7 14.1 - - + -
96H TYR* 3.9 15.7 - - - -
112H VAL* 4.1 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H GLY 3.8 6.1 - - - +
17H SER* 3.6 11.2 - - - -
68H GLY 5.5 2.3 + - - +
69H ARG* 2.7 42.1 + - - +
70H PHE* 3.8 7.4 - - - -
71H THR* 4.6 10.7 - - - +
84H GLN* 3.0 22.1 + - - +
85H MET* 1.4 80.5 - - - +
87H SER* 1.3 75.9 + - - +
88H LEU 3.1 3.7 + - - -
----------------------------------------------------------
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