Contacts of the strand formed by residues 112 - 123 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASP* 2.7 40.4 + - - +
111A HIS* 1.3 81.8 - - - +
113A PHE* 1.2 63.0 - - - -
120B ARG* 5.1 0.2 - - - -
121B LYS 3.0 9.6 - - - -
122B TYR* 3.5 23.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
105A GLU* 3.4 17.3 - - - +
107A ARG 3.7 2.9 - - - +
108A GLN* 3.7 41.7 - - + -
109A ASP 4.4 10.3 - - - -
110A GLU 5.6 1.3 - - - -
111A HIS* 4.3 16.4 - - - -
112A GLY* 1.2 78.6 - - - -
114A ILE* 1.3 63.8 + - - +
120B ARG* 3.3 2.1 - - - +
121B LYS* 2.7 62.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLU* 2.8 8.9 - - - +
106A GLU* 2.6 37.8 + - + -
107A ARG* 2.8 49.7 + - + +
109A ASP* 4.1 5.4 - - + +
113A PHE* 1.3 76.0 - - - +
115A SER* 1.3 59.7 + - - +
80B ASP* 3.1 38.8 - - - +
118B PHE* 4.8 7.0 - - + -
119B HIS 3.7 3.8 - - - +
120B ARG* 3.3 42.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LYS* 5.2 10.1 - - - -
104A HIS 3.3 13.0 - - - -
105A GLU* 2.6 23.0 + - - -
106A GLU* 3.8 4.0 - - - +
114A ILE* 1.3 73.8 - - - +
116A ARG* 1.3 63.7 + - - +
117A GLU* 5.6 2.7 - - - -
118B PHE* 3.5 8.3 - - - -
119B HIS* 2.7 48.3 + - - +
121B LYS* 2.9 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 5.6 4.6 - - - +
83A HIS* 4.3 11.5 + - - +
84A PHE* 3.6 25.6 - - + -
103A LYS* 4.3 0.2 - - - +
104A HIS* 2.8 37.9 + - - +
106A GLU* 2.8 47.9 + - + +
115A SER* 1.3 76.0 - - - +
117A GLU* 1.3 76.4 + - - +
118A PHE* 3.6 25.0 - - - -
82B LYS* 5.8 4.8 - - - +
116B ARG* 4.0 11.1 - - + +
117B GLU 3.2 13.5 - - - +
118B PHE* 3.7 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 4.2 0.4 - - - -
101A HIS* 2.6 31.8 + - + +
102A GLY 3.2 7.6 - - - +
103A LYS* 3.7 26.7 - - + +
115A SER* 5.6 3.2 - - - -
116A ARG* 1.3 81.0 - - - +
118A PHE* 1.3 64.7 - - - +
119A HIS* 5.9 0.7 - - + -
101B HIS* 5.9 0.5 - - - -
116B ARG* 3.2 10.6 - - - +
117B GLU* 2.8 63.3 + - + +
119B HIS* 5.0 12.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP 5.2 0.4 - - - -
81A VAL* 3.9 30.0 - - + +
82A LYS* 4.6 31.2 - - + -
83A HIS 4.7 3.8 - - - -
84A PHE* 3.5 32.9 - + + -
100A VAL 3.6 0.9 - - - +
101A HIS* 3.5 2.8 - - - -
102A GLY 2.7 37.8 + - - +
116A ARG* 3.6 34.1 - - - -
117A GLU* 1.3 75.8 - - - +
119A HIS* 1.3 61.6 + - - +
120A ARG 4.2 0.2 - - - -
106B GLU* 4.4 11.9 - - + -
107B ARG* 5.1 7.0 - - - -
114B ILE* 4.8 10.1 - - + -
115B SER 3.5 12.3 - - - -
116B ARG* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LYS* 5.7 1.5 - - + +
99A GLU* 2.6 34.0 + - + -
100A VAL 3.2 19.1 - - - -
101A HIS* 4.5 17.9 - + + -
117A GLU* 4.2 0.9 - - + -
118A PHE* 1.3 76.4 - - - +
120A ARG* 1.3 65.8 + - - +
121A LYS* 3.7 25.8 + - + +
113B PHE 4.2 0.2 - - - +
114B ILE* 3.7 1.5 - - - -
115B SER* 2.7 47.2 + - - +
117B GLU* 5.0 13.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASN* 3.0 18.8 + - - +
79A LEU* 3.6 17.3 - - + -
80A ASP* 2.7 52.4 + - - +
81A VAL* 5.9 0.4 - - + +
98A ILE 4.8 0.2 - - - -
99A GLU* 3.2 8.0 - - - +
100A VAL* 3.0 45.1 + - + +
118A PHE 4.2 0.2 - - - -
119A HIS* 1.3 76.7 - - - +
121A LYS* 1.3 62.9 + - - +
122A TYR* 2.8 40.2 + - + -
109B ASP* 3.0 23.0 + - - -
113B PHE 3.3 12.6 - - - +
114B ILE* 3.3 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLU* 4.0 11.4 - - + +
119A HIS* 3.7 27.1 - - + +
120A ARG* 1.3 75.3 - - - +
122A TYR* 1.3 63.0 + - - +
105B GLU* 2.7 41.7 + - - -
111B HIS 3.8 0.9 - - - +
112B GLY* 3.0 1.4 - - - -
113B PHE* 2.7 63.9 + - + +
115B SER* 2.9 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 3.4 26.4 - - + +
78A ASN 5.0 0.3 + - - -
79A LEU* 3.5 25.6 - - + -
97A VAL* 3.3 11.8 - - - +
98A ILE* 3.0 43.7 + - + +
99A GLU* 4.4 1.1 - - - +
120A ARG* 2.8 36.0 + - - -
121A LYS* 1.3 75.5 - - - +
123A ARG* 1.3 60.6 + - - +
124A ILE* 3.6 22.2 - - + -
109B ASP* 2.6 27.9 + - - -
110B GLU* 4.5 8.3 - - + +
111B HIS 3.2 20.2 - - - -
112B GLY* 3.7 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ASP* 2.7 40.0 + - + +
97A VAL* 3.9 8.1 - - + -
122A TYR* 1.3 76.7 - - - +
124A ILE* 1.3 65.6 + - - +
125A PRO* 4.0 14.4 - - + +
111B HIS* 3.1 24.3 + - + +
----------------------------------------------------------
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