Contacts of the helix formed by residues 108 - 118 (chain B) in PDB entry 4NFT
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 108 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 4.2 10.5 - - + -
9B TYR* 3.5 48.7 - - + +
100B SER* 3.4 5.8 - - - +
106B GLN 3.7 0.9 - - - +
107B PHE* 1.3 92.3 - - + +
109B VAL* 1.3 65.6 + - - +
110B GLY 3.5 0.9 - - - +
111B ARG* 3.7 29.6 - - + +
112B ILE* 3.2 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ARG* 3.5 50.3 - - + +
100B SER* 3.1 31.2 + - - +
103B ALA* 5.0 0.2 - - + -
105B LEU* 4.5 6.3 - - + -
107B PHE 4.3 3.8 - - - +
108B PRO* 1.3 69.6 - - - +
110B GLY* 1.3 60.0 + - - +
112B ILE* 3.3 5.7 + - - +
113B HIS* 2.9 27.7 + - - +
131B ALA* 3.9 2.3 - - + +
132B VAL* 3.9 29.6 - - + +
135B ALA* 4.3 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ARG* 4.8 9.7 - - - +
108B PRO* 3.5 0.6 - - - +
109B VAL* 1.3 78.1 - - - +
111B ARG* 1.3 61.5 + - - +
113B HIS* 3.2 8.6 + - - +
114B ARG* 3.2 45.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLU* 3.8 25.7 + - - +
5B SER* 2.5 34.9 + - - +
6B TYR* 3.5 23.9 + - + -
9B TYR* 3.6 25.9 + - - +
108B PRO* 3.5 27.2 + - + +
109B VAL 3.3 0.8 - - - -
110B GLY* 1.3 74.9 - - - +
112B ILE* 1.3 58.0 + - - +
114B ARG* 3.4 18.0 + - - +
115B HIS* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 3.9 18.8 - - + +
39B PHE* 4.2 10.5 - - + -
107B PHE* 4.0 17.5 - - + -
108B PRO* 3.2 21.3 + - + +
109B VAL 3.8 2.9 - - - +
110B GLY 3.2 0.2 - - - -
111B ARG* 1.3 74.4 - - - +
113B HIS* 1.3 61.5 + - - +
115B HIS* 3.5 5.5 - - - +
116B LEU* 2.8 30.1 + - + +
131B ALA* 3.8 23.3 - - + +
134B SER* 3.9 18.4 - - - -
135B ALA* 3.6 27.4 - - + -
138B LEU* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ARG* 3.6 22.6 + - - +
109B VAL 2.9 13.4 + - - +
110B GLY* 3.4 11.9 - - - +
112B ILE* 1.3 77.9 - - - +
114B ARG* 1.3 61.3 + - + +
116B LEU* 3.3 6.4 + - - +
117B LYS* 3.0 62.5 + - + +
126B VAL* 3.8 34.7 + - + +
127B GLY 4.1 6.3 + - - -
128B ALA* 5.3 3.1 - - - -
131B ALA* 3.7 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLY* 3.2 38.5 + - - +
111B ARG* 3.8 21.6 - - - +
113B HIS* 1.3 79.4 - - + +
115B HIS* 1.3 65.8 + - - +
117B LYS* 3.4 22.1 + - - +
118B SER* 3.1 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.4 27.8 - - + +
2B ARG 4.4 0.8 + - - -
4B GLU* 3.2 38.6 + - + +
6B TYR* 3.0 24.9 + + - +
36B ASN* 3.7 15.5 - - - -
39B PHE* 3.3 30.2 - + + -
111B ARG 3.0 18.4 + - - +
112B ILE 3.5 5.4 - - - +
113B HIS 3.3 0.2 - - - -
114B ARG* 1.3 77.4 - - - +
116B LEU* 1.3 59.7 + - - +
118B SER* 2.9 28.0 + - - -
119B ARG* 3.4 15.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 3.7 20.8 - - + -
43B ALA* 4.0 18.4 - - + -
58B ILE* 4.5 18.1 - - + +
63B ILE* 4.5 13.0 - - + -
112B ILE 2.8 16.5 + - - +
113B HIS 3.4 9.2 - - - +
115B HIS* 1.3 77.2 - - - +
117B LYS* 1.3 61.6 + - - +
119B ARG* 3.0 16.9 + - - +
120B THR* 3.3 10.2 + - - -
126B VAL* 3.9 26.4 - - + +
130B ALA* 4.1 13.2 - - + +
131B ALA* 4.1 11.0 - - + -
134B SER* 3.7 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B HIS* 3.0 45.6 + - + +
114B ARG* 3.8 17.4 - - - +
115B HIS 3.4 0.4 - - - -
116B LEU* 1.3 75.9 - - - +
118B SER* 1.3 59.3 + - - +
120B THR* 3.1 31.0 - - + +
125B ARG* 5.6 0.7 - - - -
126B VAL* 3.5 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLU* 5.0 1.6 + - - -
114B ARG 3.1 13.3 + - - -
115B HIS* 2.9 22.2 + - - -
116B LEU 3.1 0.6 - - - -
117B LYS* 1.3 78.0 - - - +
119B ARG* 1.3 78.8 + - - +
120B THR 3.3 4.0 - - - +
----------------------------------------------------------
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