Contacts of the strand formed by residues 106 - 114 (chain A) in PDB entry 4GK6
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 ARG 106 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 3.2 33.4 - - + -
25A LEU 3.4 7.6 - - - +
26A TYR* 3.6 28.7 + - + -
60A ARG* 3.5 41.5 + - - +
64A ALA* 5.4 2.3 - - - +
69A LEU* 5.1 3.8 - - - +
104A GLY 3.6 0.8 + - - +
105A ASP* 1.3 75.8 - - - +
107A ILE* 1.3 62.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU 3.0 11.8 + - - +
26A TYR 3.9 5.2 - - - +
27A SER* 3.8 24.9 - - - +
41A VAL* 4.0 18.4 - - + -
43A THR* 4.3 14.4 - - + -
59A PRO* 5.1 3.5 - - - +
60A ARG* 4.5 5.6 + - - -
69A LEU* 4.4 12.9 - - + +
71A ILE* 5.0 2.6 - - - +
88A VAL* 4.4 10.3 - - + -
90A LEU* 3.8 36.1 - - + +
101A ILE* 3.9 29.6 - - + -
105A ASP* 3.7 9.0 - - + +
106A ARG* 1.3 79.1 - - - +
108A ALA* 1.3 69.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 3.5 4.5 - - - -
25A LEU* 2.9 31.0 + - + +
57A VAL* 3.8 22.2 - - + -
58A HIS 3.4 13.5 - - - +
60A ARG* 3.5 16.4 - - - +
71A ILE* 4.2 7.2 - - + -
88A VAL* 4.2 14.1 - - + -
107A ILE* 1.3 83.3 - - + +
109A GLN* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY* 3.6 20.0 + - - -
23A VAL 3.2 13.5 - - - +
24A ASP* 4.0 12.8 - - - +
25A LEU* 4.5 2.9 - - - +
56A LEU 3.5 1.0 - - - +
57A VAL* 3.4 4.9 - - - -
58A HIS* 2.9 53.0 + - + +
59A PRO 3.3 18.8 + - - +
60A ARG* 4.1 13.1 - - + +
61A SER 4.9 2.4 - - - +
108A ALA* 1.3 76.6 - - - +
110A LEU* 1.3 60.5 + - - +
111A LEU* 4.0 11.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
1A LEU* 4.0 27.1 - - + -
3A ILE* 6.1 1.1 - - + -
15A ARG* 5.0 1.2 + - - -
21A ALA 4.0 1.0 - - - +
22A GLY* 3.4 2.4 - - - -
23A VAL* 2.8 44.5 + - + +
25A LEU* 4.2 24.0 - - + +
45A ILE* 5.4 0.9 - - + -
47A VAL* 4.2 18.6 - - + -
49A ILE* 5.0 2.7 - - + -
55A GLY* 4.1 4.3 - - - -
56A LEU 3.5 10.5 - - - +
57A VAL* 4.3 4.5 - - + +
78A ILE* 3.7 27.8 - - + -
109A GLN* 1.3 72.5 - - - +
111A LEU* 1.3 80.8 + - - +
112A VAL* 4.6 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 3.6 34.3 - - + +
22A GLY* 4.0 11.4 - - - +
55A GLY* 3.4 4.9 - - - -
56A LEU* 2.8 47.3 + - + +
58A HIS* 3.8 40.6 - - + +
109A GLN* 4.0 14.8 - - + -
110A LEU* 1.3 79.8 - - - +
112A VAL* 1.3 67.2 + - - +
113A GLN* 4.3 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 4.1 27.1 - - + -
15A ARG* 5.6 8.3 - - - +
21A ALA 4.8 2.4 + - - -
49A ILE* 4.2 17.0 - - + -
50A PRO* 4.8 5.2 - - + -
53A MET* 3.8 30.1 - - + -
54A VAL 3.5 7.9 - - - +
110A LEU* 4.6 7.0 - - + +
111A LEU* 1.3 80.5 - - - +
113A GLN* 1.3 69.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A MET* 3.2 9.3 - - - +
54A VAL* 2.8 41.0 + - + +
56A LEU* 3.3 26.3 - - + +
111A LEU* 5.4 10.0 - - + +
112A VAL* 1.3 81.8 - - - +
114A GLN* 1.3 70.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A SER 5.4 0.5 - - - +
52A GLY* 3.5 15.8 - - - +
53A MET* 3.7 29.4 - - - +
54A VAL* 4.4 1.6 - - - +
113A GLN* 1.3 85.8 - - - +
115A VAL* 1.3 61.2 + - - +
----------------------------------------------------------
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