Contacts of the strand formed by residues 112 - 123 (chain B) in PDB entry 2KLR
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 GLY 112 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS 3.0 9.6 - - - -
122A TYR* 3.6 21.7 - - - -
109B ASP* 2.7 41.8 + - - +
111B HIS* 1.3 82.1 - - - +
113B PHE* 1.2 64.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ARG* 3.3 2.3 - - - +
121A LYS* 2.7 61.2 + - + +
105B GLU* 3.4 17.5 - - - +
107B ARG 3.7 2.7 - - - -
108B GLN* 3.7 41.5 - - + -
109B ASP 4.3 10.8 - - - -
110B GLU 5.6 1.1 - - - -
111B HIS* 4.4 16.6 - - - -
112B GLY* 1.2 78.4 - - - -
114B ILE* 1.3 63.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP* 3.1 38.1 - - - +
118A PHE* 4.8 7.2 - - + -
119A HIS 3.7 4.0 - - - +
120A ARG* 3.3 42.4 - - + +
105B GLU* 2.8 7.9 - - - +
106B GLU* 2.6 38.2 + - + -
107B ARG* 2.8 49.6 + - + +
109B ASP* 4.1 5.2 - - - +
113B PHE* 1.3 75.9 - - - +
115B SER* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 3.5 8.8 - - - -
119A HIS* 2.7 47.5 + - - +
121A LYS* 2.9 16.6 + - - +
103B LYS* 5.2 9.6 - - - -
104B HIS 3.3 13.5 - - - -
105B GLU* 2.6 23.4 + - - -
106B GLU* 3.8 3.6 - - - +
114B ILE* 1.3 75.0 - - - +
116B ARG* 1.3 63.7 + - - +
117B GLU* 5.6 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 5.8 5.0 - - - +
116A ARG* 4.0 10.2 - - + +
117A GLU 3.2 13.7 - - - +
118A PHE* 3.7 26.0 - - + -
82B LYS* 5.6 4.8 - - - +
83B HIS* 4.3 11.7 + - - +
84B PHE* 3.6 25.7 - - + -
103B LYS* 4.2 0.7 - - - +
104B HIS* 2.8 36.5 + - - +
106B GLU* 2.8 45.3 + - + +
115B SER* 1.3 76.8 - - - +
117B GLU* 1.3 74.6 + - - +
118B PHE* 3.6 25.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A HIS* 5.8 0.7 - - - -
116A ARG* 3.2 10.8 - - - +
117A GLU* 2.8 62.7 + - + +
119A HIS* 5.0 13.5 + - + +
84B PHE* 4.2 0.2 - - - -
101B HIS* 2.6 30.8 + - + +
102B GLY 3.2 7.9 - - - +
103B LYS* 3.7 27.4 - - + +
115B SER* 5.6 2.9 - - - -
116B ARG* 1.3 80.6 - - - +
118B PHE* 1.3 65.8 + - - +
119B HIS* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU* 4.4 12.1 - - + -
107A ARG* 5.1 7.6 - - - -
114A ILE* 4.8 9.4 - - + -
115A SER 3.5 13.5 - - - -
116A ARG* 3.7 26.0 - - + -
80B ASP 5.2 0.2 - - - -
81B VAL* 3.9 29.6 - - + +
82B LYS* 4.6 31.2 - - + -
83B HIS 4.7 4.7 - - - -
84B PHE* 3.5 32.9 - + + -
100B VAL 3.6 1.0 - - - +
101B HIS* 3.5 2.5 - - - -
102B GLY 2.7 36.8 + - - +
116B ARG* 3.6 34.1 - - - -
117B GLU* 1.3 75.8 - - - +
119B HIS* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ILE* 3.7 1.3 - - - -
115A SER* 2.7 49.7 + - - +
117A GLU* 5.0 13.0 + - + +
92B LYS* 5.7 1.5 - - + +
99B GLU* 2.6 33.9 + - + -
100B VAL 3.2 20.2 - - - -
101B HIS* 4.5 19.3 - + + -
117B GLU* 4.2 1.3 - - + -
118B PHE* 1.3 77.3 - - - +
120B ARG* 1.3 65.6 + - - +
121B LYS* 3.7 26.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASP* 2.9 22.4 + - - -
113A PHE 3.3 14.8 - - - +
114A ILE* 3.3 22.8 - - + +
78B ASN* 3.0 19.5 + - - +
79B LEU* 3.6 17.3 - - + -
80B ASP* 2.7 51.4 + - - +
81B VAL* 5.9 0.4 - - + +
98B ILE 4.8 0.2 - - - -
99B GLU* 3.2 7.8 - - - +
100B VAL* 3.0 46.0 + - + +
119B HIS* 1.3 77.4 - - - +
121B LYS* 1.3 60.9 + - - +
122B TYR* 2.8 39.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLU* 2.7 33.0 + - - -
111A HIS 3.8 0.5 - - - +
112A GLY* 3.0 1.6 - - - -
113A PHE* 2.7 62.4 + - + +
115A SER* 2.9 22.4 + - - -
99B GLU* 4.0 11.2 - - + +
119B HIS* 3.7 27.1 + - + +
120B ARG* 1.3 75.7 - - - +
122B TYR* 1.3 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASP* 2.6 27.5 + - - -
110A GLU* 4.4 9.1 - - + +
111A HIS 3.2 19.3 - - - -
112A GLY* 3.6 10.8 - - - -
77B VAL* 3.4 26.8 - - + +
78B ASN 3.8 0.3 + - - -
79B LEU* 3.5 26.2 - - + -
97B VAL* 3.3 11.8 - - - +
98B ILE* 3.0 45.4 + - + +
99B GLU* 4.5 0.7 - - - +
120B ARG* 2.8 35.8 + - + -
121B LYS* 1.3 75.5 - - - +
123B ARG* 1.3 58.4 + - - +
124B ILE* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A HIS* 3.1 23.3 + - - +
96B ASP* 2.7 40.7 + - + +
97B VAL* 3.9 8.1 - - + -
122B TYR* 1.3 74.6 - - - +
124B ILE* 1.3 66.9 + - - +
125B PRO* 4.0 14.6 - - + +
----------------------------------------------------------
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