Contacts of the helix formed by residues 109 - 118 (chain A) in PDB entry 4NAK
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 ALA 109 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 4.1 3.5 - - - +
85A ALA* 4.6 0.2 - - + -
99A GLN* 2.8 22.4 + - + +
100A TYR* 4.2 12.6 - - + -
107A PRO* 3.1 1.5 + - + -
108A ILE* 1.3 72.3 - - - +
110A LEU* 1.3 60.7 + - + +
111A TYR 3.5 0.5 + - - -
112A SER* 3.8 2.1 + - - -
113A PHE* 3.5 16.3 + - - +
136A ILE* 5.7 0.2 - - + -
137A PHE* 3.7 29.3 - - + -
180A SER* 4.0 21.8 - - - +
411A K 3.5 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLN* 3.7 18.2 - - + -
107A PRO* 2.9 35.3 + - + +
109A ALA* 1.3 76.6 - - - +
111A TYR* 1.3 63.6 + - - +
112A SER 3.5 0.2 - - - -
113A PHE* 3.4 25.5 - - + +
114A PHE* 3.0 33.6 + - + -
136A ILE* 3.8 34.1 - - + +
137A PHE* 4.0 11.7 - - + -
140A TYR* 3.7 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 2.6 53.4 + - + -
104A LEU* 3.8 9.4 + - - +
106A GLN* 3.4 34.1 - - - +
107A PRO 3.9 4.3 - - - -
108A ILE* 3.2 14.4 + - - +
110A LEU* 1.3 78.5 - - - +
112A SER* 1.3 62.2 + - - +
114A PHE* 3.4 3.5 + - - +
115A THR* 3.1 24.9 + - - -
183A PRO* 3.4 29.4 - - + +
184A LEU* 5.6 0.7 - - + -
298A LEU* 3.7 38.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.6 10.7 - - - +
109A ALA 3.8 1.0 + - - -
111A TYR* 1.3 75.4 - - - +
113A PHE* 1.3 68.2 + - - +
115A THR* 3.6 8.0 - - - -
116A PHE* 2.9 37.5 + - - -
178A HIS* 3.4 36.5 - - - -
180A SER* 4.2 0.2 - - - -
182A ARG 3.9 4.9 - - - -
183A PRO* 4.0 3.2 + - - -
185A VAL* 4.2 6.5 - - - -
411A K 2.6 23.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.9 18.8 - - + +
109A ALA 3.5 14.2 + - - +
110A LEU* 3.4 27.8 - - + +
112A SER* 1.3 81.3 + - - +
114A PHE* 1.3 76.0 + + - +
116A PHE* 4.6 2.7 - - - -
117A SER* 3.0 27.2 + - - -
125A ILE* 3.5 25.9 - - + +
127A VAL* 3.9 9.0 - - + -
137A PHE* 3.7 34.5 - + + -
140A TYR* 4.6 2.2 - - + -
144A ILE* 3.8 32.3 - - + -
148A LEU* 3.8 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLN* 3.3 31.2 - - - -
110A LEU* 3.0 35.7 + - + +
111A TYR 3.9 3.4 - - - +
113A PHE* 1.3 83.4 - + - +
115A THR* 1.3 67.1 + - - +
117A SER* 2.7 26.7 + - - +
118A ARG* 3.2 30.0 + - + +
140A TYR* 3.6 54.1 - + + -
143A SER* 5.4 0.9 - - - -
144A ILE* 4.1 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A TYR 3.1 16.0 + - - -
112A SER* 3.2 12.4 + - - -
114A PHE* 1.3 76.9 - - - +
116A PHE* 1.3 63.1 + - + +
118A ARG* 3.5 24.1 + - - +
119A MET* 3.4 17.6 + - - +
183A PRO 5.0 2.3 + - - -
185A VAL* 3.9 24.2 + - + +
187A THR* 3.7 30.7 + - - +
190A VAL* 4.6 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 3.8 34.8 - - + -
83A LEU* 4.4 4.0 - - + -
112A SER* 2.9 34.7 + - - +
113A PHE* 3.9 6.3 - - - +
115A THR* 1.3 72.5 - - + +
117A SER* 1.3 63.5 + - - +
119A MET* 3.1 17.7 + - - +
122A VAL* 3.5 21.5 - - + +
125A ILE* 4.0 12.1 - - + -
176A CYS* 3.9 13.7 - - - -
178A HIS* 3.6 50.3 - + + -
185A VAL* 4.7 2.2 - - + -
190A VAL* 3.7 39.5 - - + -
237A PRO* 3.9 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 3.0 17.0 + - - -
114A PHE* 2.7 32.5 + - - -
116A PHE* 1.3 76.2 - - - +
118A ARG* 1.3 61.1 + - - +
125A ILE* 4.0 3.3 - - - +
144A ILE* 4.0 29.6 - - - +
145A ASP* 4.2 12.2 + - - +
146A VAL* 3.6 20.1 - - - +
412A K 3.1 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE* 3.2 36.9 + - + +
115A THR* 3.5 24.2 + - - +
116A PHE 3.2 0.6 - - - -
117A SER* 1.3 80.3 + - - +
119A MET* 1.3 63.0 + - + +
120A PRO* 3.4 9.7 - - - +
145A ASP* 6.0 0.4 - - - -
187A THR* 4.2 13.7 + - - -
412A K 4.4 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