Contacts of the helix formed by residues 95 - 99 (chain N) in PDB entry 2WQT
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 PRO 95 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88N TYR* 3.5 23.1 - - + +
93N ILE* 3.9 6.7 - - + +
94N ILE* 1.4 87.0 - - + +
96N PHE* 1.3 67.0 + - - +
97N SER* 4.2 12.8 - - - +
98N ARG* 3.1 26.1 + - + +
99N VAL 4.5 0.9 + - - -
259N PHE* 4.8 0.5 - - - -
260N SER* 3.4 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 96 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94N ILE 3.2 4.2 + - - -
95N PRO* 1.3 71.4 - - - +
97N SER* 1.3 64.8 + - - +
98N ARG 3.4 0.5 + - - -
99N VAL* 3.7 15.8 + - - +
102N PRO* 4.0 21.9 - - + +
239N VAL* 3.6 31.2 - - + -
240N ASN* 3.6 5.2 - - - -
241N ALA* 3.3 39.9 - - + -
259N PHE* 4.5 10.6 - + + -
260N SER* 3.0 30.2 + - - +
261N SER 4.7 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 97 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E LEU* 5.0 19.8 - - - +
95N PRO* 4.2 10.0 - - - +
96N PHE* 1.3 80.4 + - - +
98N ARG* 1.3 63.7 + - - +
99N VAL* 3.3 5.0 + - - -
100N LEU 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E HIS* 5.4 5.6 - - - -
5E THR* 5.5 10.2 + - - -
54N ARG* 4.1 4.4 - - - +
85N ASP* 3.1 49.3 + - - +
86N MET* 3.9 10.7 - - - +
88N TYR* 3.0 33.6 + - - +
94N ILE* 4.7 2.5 - - + -
95N PRO* 3.1 29.6 + - + +
97N SER* 1.3 80.7 + - - +
99N VAL* 1.3 63.1 + - + +
100N LEU 4.1 1.0 + - - -
162N GLY 4.9 0.4 + - - -
163N VAL* 3.6 23.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94N ILE* 5.5 2.2 - - + -
95N PRO 4.5 0.6 + - - -
96N PHE 3.7 13.8 + - - +
97N SER* 4.4 3.0 - - - +
98N ARG* 1.3 95.8 - - + +
100N LEU* 1.3 64.6 + - - +
101N GLN 3.5 2.4 + - - -
102N PRO* 3.6 25.0 - - + +
139N VAL* 4.1 7.6 - - + -
140N VAL 3.7 11.0 - - - +
141N GLY* 3.6 28.5 - - - +
143N ARG* 5.2 1.6 - - - +
162N GLY* 3.8 24.2 - - - -
163N VAL* 3.9 18.8 - - + +
259N PHE* 6.0 1.3 - - + -
----------------------------------------------------------
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