Contacts of the strand formed by residues 111 - 116 (chain Q) in PDB entry 1NVU
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 MET 111 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78Q PHE* 3.0 18.2 - - + +
80Q CYS* 3.8 20.2 - - - -
97Q ARG* 4.1 25.8 - - + +
100Q ILE* 3.7 42.2 - - + -
109Q VAL* 3.2 21.4 + - + +
110Q PRO* 1.3 75.4 - - - +
112Q VAL* 1.3 60.8 + - - +
137Q TYR* 5.4 1.3 - - - -
139Q ILE* 3.4 45.3 - - + +
140Q PRO* 3.7 0.3 - - - +
159Q LEU* 3.7 2.7 - - - -
162Q GLU* 2.6 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78Q PHE 3.0 4.4 + - - -
79Q LEU* 3.6 11.7 - - + -
80Q CYS* 2.9 26.6 + - - +
111Q MET* 1.3 81.9 - - - +
113Q LEU* 1.3 73.5 + - - +
114Q VAL* 3.6 11.0 + - + +
139Q ILE* 4.2 3.1 - - - -
140Q PRO* 3.8 19.5 - - + +
142Q ILE* 4.1 23.6 - - + -
155Q ALA* 4.0 6.1 - - - +
158Q THR* 4.2 3.1 - - + -
159Q LEU* 3.7 37.7 - - + +
162Q GLU* 3.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80Q CYS* 3.6 17.5 - - + +
82Q PHE* 3.9 22.7 - - + -
93Q ILE* 3.9 28.7 - - + -
112Q VAL* 1.3 75.2 - - - +
114Q VAL* 1.3 60.1 + - - +
130Q ALA* 3.4 29.6 - - + +
133Q LEU* 4.5 10.1 - - + -
134Q ALA* 4.1 12.6 - - + +
137Q TYR* 5.8 1.8 - - + -
139Q ILE* 3.8 15.9 - - + +
140Q PRO 3.0 14.6 + - - +
141Q TYR* 3.4 18.8 - - + -
142Q ILE 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Q LEU* 4.1 16.4 - - + -
79Q LEU* 3.7 30.5 - - + -
80Q CYS 2.8 13.8 + - - +
81Q VAL* 3.4 8.1 - - + -
82Q PHE* 3.0 34.2 + - - +
112Q VAL* 4.0 14.1 - - + +
113Q LEU* 1.3 78.6 - - - +
115Q GLY* 1.3 62.9 + - - +
116Q ASN 4.2 1.1 - - - +
142Q ILE 3.3 7.9 - - - +
144Q THR* 3.5 31.0 - - + +
155Q ALA* 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 115 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82Q PHE* 3.6 28.0 - - - -
84Q ILE* 3.8 6.1 - - - +
114Q VAL* 1.3 70.6 - - - +
116Q ASN* 1.3 62.9 + - - +
118Q CYS* 4.5 0.7 - - - +
141Q TYR* 3.6 13.6 - - - -
142Q ILE 3.0 11.1 + - - -
143Q GLU* 3.2 8.1 - - - +
144Q THR* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 116 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Q VAL 3.0 25.8 + - - +
15Q GLY* 3.6 7.7 - - - -
19Q LEU* 3.4 20.8 - - + +
81Q VAL* 3.9 11.9 - - + -
82Q PHE 2.7 16.9 + - - +
83Q ALA* 3.5 0.6 - - - -
84Q ILE* 3.0 22.5 + - - +
114Q VAL* 3.6 1.0 + - + -
115Q GLY* 1.3 73.7 - - - +
117Q LYS* 1.3 80.6 + - - +
118Q CYS 3.3 1.7 + - - -
144Q THR* 2.7 30.7 + - - +
146Q ALA 3.5 4.9 + - - -
1001Q GTP 3.2 24.6 + - - -
----------------------------------------------------------
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