Contacts of the helix formed by residues 96 - 110 (chain C) in PDB entry 4WFN
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 96 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C TYR* 5.9 0.4 - - + -
94C THR 3.6 6.0 - - - +
95C LEU* 1.3 99.3 - - + +
97C ARG* 1.3 60.5 + - - +
98C GLN* 3.2 5.8 - - + +
99C VAL* 3.0 35.7 + - + +
100C ARG 3.1 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C LEU 3.3 3.8 + - - -
96C PRO* 1.3 68.3 - - - +
98C GLN* 1.3 67.2 - - + +
100C ARG* 2.9 41.0 + - + +
101C GLN* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C PRO* 3.2 4.9 + - + -
97C ARG* 1.3 77.7 - - + +
99C VAL* 1.3 63.2 + - + +
101C GLN* 3.5 19.0 - - - +
102C LEU* 2.9 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C VAL* 3.5 31.0 - - + -
29C GLU* 4.7 12.6 - - - +
30C VAL* 3.9 13.7 - - + +
95C LEU* 4.5 11.9 - - + -
96C PRO* 3.0 27.1 + - + +
98C GLN* 1.3 80.0 - - + +
100C ARG* 1.3 60.5 + - - +
102C LEU* 3.9 11.0 - - + -
103C GLY* 3.0 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 5.6 3.1 - - - +
33C TRP* 3.2 49.3 - - + -
93C TYR 4.7 0.4 + - - -
94C THR* 3.7 25.1 - - - +
95C LEU* 3.1 47.6 + - + +
96C PRO 3.1 4.8 + - - +
97C ARG* 2.9 39.2 + - + +
99C VAL* 1.3 79.6 - - - +
101C GLN* 1.3 58.9 + - - +
103C GLY* 4.1 2.6 + - - -
104C LEU* 3.9 12.5 + - - +
177C VAL* 5.0 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ARG* 2.9 39.1 + - + +
98C GLN* 3.5 19.3 - - - +
100C ARG* 1.3 76.2 - - - +
102C LEU* 1.3 62.1 + - - +
103C GLY 3.2 1.3 - - - -
104C LEU* 3.2 22.2 - - + +
105C ALA* 3.8 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PRO* 4.3 8.6 - - + +
26C VAL* 4.3 13.2 - - + -
98C GLN* 2.9 22.8 + - + +
99C VAL* 3.3 16.1 + - + +
101C GLN* 1.3 77.1 - - - +
103C GLY* 1.3 68.5 + - - +
105C ALA* 3.6 5.5 + - - +
106C MET* 3.0 53.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C VAL* 4.9 3.8 - - - -
27C LEU* 4.9 3.5 - - - +
30C VAL* 4.1 17.7 - - - -
99C VAL 3.0 16.4 + - - -
100C ARG 4.6 1.1 - - - -
101C GLN 3.2 0.4 - - - -
102C LEU* 1.3 79.6 - - - +
104C LEU* 1.3 54.6 - - - +
106C MET* 2.5 30.7 + - - +
107C ALA* 2.9 9.7 + - - +
177C VAL* 4.3 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C ARG 3.9 5.5 + - - +
101C GLN* 3.2 41.7 - - + +
103C GLY* 1.3 72.5 - - - +
105C ALA* 1.3 66.3 + - + +
107C ALA* 3.0 9.1 + - - +
108C ILE* 2.9 35.9 + - + +
175C VAL* 3.7 37.2 - - + +
177C VAL* 3.8 25.7 - - + +
180C ILE* 4.3 2.4 - - + +
193C LEU* 5.2 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 6.5 0.9 - - + -
17C LEU* 4.7 3.6 - - + +
18C PRO* 3.5 23.2 - - + +
101C GLN 3.8 11.2 - - - +
102C LEU* 3.6 8.0 + - - +
104C LEU* 1.3 83.2 - - + +
106C MET* 1.3 56.8 + - - +
108C ILE* 3.3 12.4 + - - +
109C ALA* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PRO* 3.5 18.6 - - + +
19C LEU 4.3 11.0 - - - +
20C PRO* 3.8 20.6 - - + +
22C VAL* 4.0 6.5 - - - +
23C ASN* 3.4 45.3 - - + +
26C VAL* 4.3 10.3 - - + -
27C LEU* 3.7 17.0 - - + -
102C LEU* 3.0 38.2 + - + +
103C GLY* 2.5 18.3 + - - +
105C ALA* 1.3 71.8 - - - +
107C ALA* 1.3 48.4 - - - -
109C ALA* 3.5 4.1 - - - +
110C SER* 2.2 37.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 5.0 2.9 - - - +
103C GLY 2.9 6.3 + - - +
104C LEU 3.2 12.3 - - - +
106C MET* 1.3 76.3 - - - +
108C ILE* 1.3 60.6 + - - +
109C ALA 3.1 1.3 - - - -
110C SER* 2.8 26.2 + - - -
111C ARG* 3.0 18.5 + - - +
177C VAL* 4.0 17.3 - - + +
180C ILE* 3.6 26.5 - - + -
181C LEU* 5.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 6.1 6.3 - - + -
17C LEU* 5.0 10.3 - - + -
104C LEU* 2.9 26.0 + - + +
105C ALA* 3.7 9.9 - - - +
107C ALA* 1.3 74.7 - - - +
109C ALA* 1.3 58.8 + - - +
111C ARG* 2.8 23.5 + - + +
112C GLN* 3.1 26.7 + - - +
116C LYS* 5.9 0.2 - - + -
175C VAL* 6.2 1.6 - - + -
180C ILE* 4.5 13.5 - - + -
186C LEU* 4.8 10.8 - - + -
188C ILE* 4.9 23.3 - - + -
193C LEU* 6.1 5.4 - - + -
194C GLU* 5.1 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 3.6 32.1 - - + +
18C PRO* 3.9 12.6 - - + +
21C GLU* 5.5 3.9 - - + +
22C VAL* 3.9 12.0 - - + +
105C ALA 2.9 17.5 + - - +
106C MET* 3.5 9.2 - - - +
108C ILE* 1.3 77.3 - - - +
110C SER* 1.3 56.6 + - - +
112C GLN* 3.0 15.9 + - - +
113C GLU* 2.9 18.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C VAL* 3.1 28.7 - - - +
27C LEU* 4.3 10.3 - - - +
106C MET 2.2 26.9 + - - -
107C ALA* 2.8 14.4 + - - -
109C ALA* 1.3 75.3 - - - +
111C ARG* 1.3 71.1 + - - +
112C GLN 3.4 0.2 - - - -
113C GLU* 2.8 24.9 + - - +
114C GLY 5.4 0.2 + - - -
181C LEU* 5.3 4.9 - - - -
----------------------------------------------------------
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