Contacts of the strand formed by residues 100 - 107 (chain A) in PDB entry 2KI6
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 ILE 100 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS* 5.5 5.4 - - + +
88A ALA* 4.3 17.9 - - + -
89A VAL 3.7 7.2 - - - +
90A TYR* 3.3 26.9 - - + -
99A ASP* 1.3 84.4 + - - +
101A ILE* 1.3 63.1 + - - +
102A GLY* 3.0 27.0 + - - +
103A GLU* 4.8 2.0 - - + +
125A SER* 5.2 0.5 - - - -
126A ALA 4.1 15.8 - - - +
127A GLU* 4.8 11.1 - - - +
128A LYS 3.6 33.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 3.2 16.8 - - + +
29A LEU* 5.2 1.6 - - + -
30A PRO* 3.6 40.7 - - + +
32A LEU* 4.6 16.6 - - + -
38A SER* 4.8 2.9 - - - +
40A PRO* 3.8 11.0 - - + -
89A VAL* 3.1 46.0 + - + +
90A TYR 3.6 3.6 - - - -
91A ASP* 3.4 36.8 - - + +
99A ASP* 3.3 6.5 + - - +
100A ILE* 1.3 73.0 - - - +
102A GLY* 1.3 55.7 + - - +
125A SER* 3.2 21.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 3.2 15.8 - - - +
89A VAL 2.7 31.0 + - - +
100A ILE* 3.0 11.4 + - - +
101A ILE* 1.3 81.7 - - - +
103A GLU* 1.3 59.9 + - - +
124A GLN 3.1 13.0 - - - -
125A SER* 3.5 5.4 - - - -
126A ALA 4.0 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 3.3 6.7 - - - +
86A VAL* 4.9 5.2 - - - +
87A MET 3.0 16.2 - - - +
88A ALA* 3.3 18.4 - - + +
89A VAL 4.3 0.2 - - - +
100A ILE* 4.8 1.7 - - + +
102A GLY* 1.3 74.6 - - - +
104A PHE* 1.3 62.8 + - - +
105A LYS* 2.5 40.1 + - - +
124A GLN* 2.7 42.6 + - + +
126A ALA* 3.4 33.0 - - + +
128A LYS* 3.1 30.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.9 20.9 - - + -
8A TYR* 3.5 34.5 - + - -
21A VAL* 5.8 0.2 - - + -
85A LEU* 5.5 8.3 - - + -
86A VAL* 3.5 0.5 - - - +
87A MET* 2.6 91.7 + - + -
103A GLU* 1.3 77.2 - - - +
105A LYS* 1.3 72.2 + - - +
106A VAL* 5.4 6.1 - - + -
121A ARG* 3.5 18.6 - - + -
122A ASP 3.8 17.7 - - - +
123A LEU* 3.4 22.0 - - + -
124A GLN* 4.6 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 5.0 9.0 - - + -
85A LEU 3.0 21.5 - - - +
86A VAL* 3.3 25.0 - - + +
103A GLU* 2.5 30.6 + - - +
104A PHE* 1.3 84.6 - - - +
106A VAL* 1.3 63.6 + - - +
107A PRO* 4.8 0.6 - - + +
121A ARG* 5.4 4.2 - - - -
124A GLN* 4.7 5.6 - - - +
126A ALA* 5.4 1.8 - - - +
128A LYS* 4.7 10.1 - - - +
107B ASN* 4.2 20.4 - - - +
108B GLY* 4.2 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 5.0 12.8 - - + +
10A LEU* 5.7 6.7 - - + -
84A THR* 3.5 10.3 - - - +
85A LEU* 3.2 31.7 + - + +
104A PHE* 5.4 5.6 - - + -
105A LYS* 1.3 78.6 - - - +
107A PRO* 1.3 76.5 - - + +
108A MET* 2.9 11.1 + - - -
110A THR* 5.8 1.1 - - - -
111A VAL* 3.7 27.1 - - + -
119A GLU* 5.8 3.1 - - - +
121A ARG* 5.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 3.6 16.3 - - + +
105A LYS* 4.8 0.9 - - + +
106A VAL* 1.3 86.1 - - + +
108A MET* 1.3 57.2 + - - +
109A ASN* 3.1 4.0 - - + +
110A THR* 2.8 46.5 + - - +
111A VAL* 3.4 9.9 + - - +
14B HIS* 4.9 13.9 - - + -
25B ASP* 6.1 0.2 - - - +
27B THR* 4.4 24.0 - - + -
28B ARG* 3.7 22.4 - - + +
----------------------------------------------------------
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