Contacts of the helix formed by residues 100 - 109 (chain Y) in PDB entry 2Q4G
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 100 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69Y ASP* 3.1 37.2 + - - +
72Y VAL* 5.2 5.7 - - - +
96Y LEU* 5.6 3.2 - - - +
97Y THR 3.0 7.7 + - - -
99Y ALA* 1.3 77.7 - - - +
101Y CYS* 1.3 58.0 + - - +
102Y GLY 3.5 0.7 - - - -
103Y VAL* 3.1 25.9 - - - +
104Y LEU* 3.7 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 101 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96Y LEU* 5.4 1.3 - - - -
97Y THR 2.9 23.2 + - - -
98Y GLY* 2.7 19.6 + - - +
100Y GLY* 1.3 77.0 - - - +
102Y GLY* 1.3 58.9 + - - +
103Y VAL 3.2 2.0 - - - -
104Y LEU* 3.7 5.6 - - - -
105Y SER* 2.8 30.3 + - - -
124Y LEU* 3.5 27.1 - - - -
128Y GLY* 3.8 14.1 - - - +
131Y LEU* 4.1 3.8 - - + -
132Y LEU* 3.2 36.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99Y ALA 3.6 6.1 + - - -
100Y GLY 3.5 1.0 - - - -
101Y CYS* 1.3 79.4 - - - +
103Y VAL* 1.3 60.9 + - - +
105Y SER* 3.6 4.1 + - - -
106Y SER* 3.4 21.5 + - - -
131Y LEU* 3.4 32.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69Y ASP 5.2 2.7 - - - +
72Y VAL* 5.9 0.2 - - + -
73Y HIS* 4.3 46.2 - - + +
76Y LEU* 5.1 2.5 - - + -
99Y ALA 4.8 1.0 + - - +
100Y GLY* 3.1 25.8 - - - +
102Y GLY* 1.3 75.1 - - - +
104Y LEU* 1.3 69.5 + - + +
106Y SER* 3.2 7.8 + - - -
107Y THR* 2.9 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72Y VAL* 4.6 6.1 - - + -
76Y LEU* 3.5 37.2 - - + -
89Y LEU* 5.5 2.5 - - + -
91Y LEU* 5.0 5.6 - - + -
96Y LEU* 4.1 15.7 - - + -
100Y GLY 3.7 11.7 - - - +
101Y CYS* 3.2 9.8 + - - +
103Y VAL* 1.3 81.5 - - - +
105Y SER* 1.3 57.5 + - - +
107Y THR* 3.2 1.4 + - - -
108Y LEU* 2.9 55.3 + - + +
117Y LEU* 5.7 0.9 - - + -
119Y LEU* 4.0 31.0 - - + -
132Y LEU* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 105 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101Y CYS 2.8 14.7 + - - -
102Y GLY* 3.6 6.3 - - - -
104Y LEU* 1.3 76.9 - - - +
106Y SER* 1.3 62.5 + - - +
108Y LEU* 3.1 20.7 + - - +
109Y ARG* 3.4 13.7 + - - +
131Y LEU 3.0 25.4 + - - -
132Y LEU* 3.3 14.1 + - - +
134Y GLU* 3.9 5.0 + - - +
135Y GLY* 2.8 31.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80Y GLN* 4.9 0.2 - - - +
102Y GLY 3.4 10.3 + - - -
103Y VAL* 3.2 9.9 + - - -
105Y SER* 1.3 75.8 + - - +
107Y THR* 1.3 65.4 + - - +
109Y ARG* 3.1 37.5 + - - +
110Y THR* 3.9 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 107 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73Y HIS* 4.9 4.3 - - - -
76Y LEU* 3.9 32.7 - - + +
80Y GLN* 3.0 47.5 + - + +
103Y VAL* 2.9 19.6 + - - +
104Y LEU* 3.2 11.0 + - - -
106Y SER* 1.3 76.7 - - - +
108Y LEU* 1.3 62.3 + - + +
109Y ARG 3.0 0.2 - - - -
110Y THR* 2.9 21.3 + - - -
111Y LEU* 3.7 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76Y LEU* 5.5 1.6 - - + -
89Y LEU* 5.8 1.6 - - + -
104Y LEU* 2.9 50.0 + - + +
105Y SER* 3.1 14.6 + - - +
107Y THR* 1.3 80.3 - - + +
109Y ARG* 1.3 60.2 + - - +
110Y THR 3.2 0.6 + - - -
111Y LEU* 3.9 18.0 + - + +
114Y LEU* 4.9 12.8 - - + -
117Y LEU* 3.9 26.9 - - + -
119Y LEU* 5.8 0.9 - - + -
132Y LEU* 4.9 6.1 - - + +
135Y GLY 5.0 5.8 - - - -
136Y LEU* 3.6 32.3 - - + -
141Y CYS* 4.2 18.5 - - - +
143Y LEU* 4.5 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105Y SER* 3.4 12.6 + - - +
106Y SER* 3.2 29.0 + - - +
107Y THR 3.0 0.6 - - - -
108Y LEU* 1.3 78.3 - - - +
110Y THR* 1.3 61.2 + - + +
111Y LEU 3.7 0.7 - - - -
134Y GLU* 3.4 37.8 + - - +
135Y GLY* 3.8 11.3 - - - -
138Y ASP* 2.7 57.1 + - + +
140Y GLN* 3.3 29.0 - - - +
141Y CYS 5.4 0.9 - - - +
----------------------------------------------------------
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