Contacts of the helix formed by residues 82 - 94 (chain A) in PDB entry 2KSP
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 PRO 82 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LYS 4.4 2.0 - - - +
81A LEU* 1.3 97.3 - - + +
83A ASN* 1.3 59.0 + - - +
84A THR* 3.1 8.1 - - - +
85A VAL* 2.8 41.9 + - + +
86A LEU* 3.0 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 5.0 8.5 - - - +
81A LEU 3.6 2.9 + - - +
82A PRO* 1.3 71.9 - - - +
84A THR* 1.3 62.3 + - - +
86A LEU* 3.2 23.6 + - - +
87A GLY* 3.1 18.7 + - - -
151B PHE* 4.1 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PRO* 4.9 5.7 - - - +
83A ASN* 1.3 78.6 + - - +
85A VAL* 1.3 65.2 + - + +
87A GLY* 3.3 3.2 + - - -
88A LYS* 3.1 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 4.4 15.7 - - + -
82A PRO* 2.8 38.5 + - + +
84A THR* 1.3 75.7 - - - +
86A LEU* 1.3 61.3 + - - +
88A LYS* 3.1 12.7 + - + +
89A ILE* 2.8 49.2 + - + +
113A ILE* 6.2 0.2 - - - -
116A LYS* 3.9 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A MET* 3.5 37.3 - - + +
77A VAL* 4.1 12.6 - - + -
81A LEU* 3.4 34.1 - - + +
82A PRO 3.0 16.8 - - - +
83A ASN* 3.2 19.9 + - - +
85A VAL* 1.3 76.9 - - + +
87A GLY* 1.3 57.0 + - - +
89A ILE* 3.3 7.4 + - + +
90A TRP* 2.9 31.5 + - - +
113A ILE* 6.3 1.8 - - + -
151B PHE* 3.4 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASN 3.1 8.8 + - - -
84A THR* 3.3 4.0 + - - -
85A VAL 3.3 0.2 - - - -
86A LEU* 1.3 78.6 - - - +
88A LYS* 1.3 56.9 + - - +
91A LYS* 3.0 22.1 + - - +
149B ASN* 2.7 35.2 + - - -
151B PHE* 3.6 15.1 - - - +
152B GLU* 5.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 3.1 30.7 + - + +
85A VAL* 3.1 13.1 + - + +
87A GLY* 1.3 74.2 - - - +
89A ILE* 1.3 67.8 + - + +
91A LYS* 3.3 7.9 + - - +
92A LEU* 3.1 36.3 + - + +
122A LEU* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A MET* 4.2 8.1 - - + -
85A VAL* 2.8 40.2 + - + +
86A LEU* 3.7 7.2 - - + +
88A LYS* 1.3 72.6 - - + +
90A TRP* 1.3 58.5 + - - +
92A LEU* 3.8 1.4 - - - +
93A ALA* 2.8 33.1 + - - +
109A ALA* 3.4 35.0 - - - +
112A LEU* 3.6 21.6 - - + +
113A ILE* 3.8 15.9 - - + +
116A LYS* 4.2 8.1 - - + -
122A LEU* 3.4 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR 4.4 1.3 - - - -
69A GLY* 3.5 23.6 - - - -
72A ALA* 3.5 18.8 - - + -
76A MET* 4.4 6.7 - - + -
86A LEU 2.9 16.8 + - - +
87A GLY 3.8 0.7 - - - +
89A ILE* 1.3 78.4 - - - +
91A LYS* 1.3 59.8 + - - +
93A ALA* 4.5 4.3 - - - -
94A ASP* 2.8 43.8 + - + +
99A GLY 3.4 25.1 - - - -
101A LEU* 3.4 44.2 - - + -
148B TYR* 2.9 22.3 + - + +
149B ASN* 3.7 25.6 - - + +
150B PRO* 3.4 20.6 - - + -
151B PHE* 3.5 18.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLY 3.0 20.0 + - - +
88A LYS* 3.3 7.8 + - - +
90A TRP* 1.3 81.0 - - - +
92A LEU* 1.3 65.9 + - + +
94A ASP* 4.5 0.9 - - - -
97A LYS* 3.5 31.1 + - + +
126A LEU* 5.7 0.2 - - - +
144B GLU 5.7 0.6 + - - -
146B LYS* 4.3 22.4 - - + +
149B ASN* 4.1 4.0 - - + +
152B GLU* 2.6 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LYS* 3.1 32.7 + - + +
89A ILE 3.8 2.2 - - - +
91A LYS* 1.3 87.1 - - + +
93A ALA* 1.3 63.5 + - - +
94A ASP 3.4 2.7 + - - +
95A VAL* 4.0 3.3 - - - +
97A LYS* 4.9 0.5 + - - -
112A LEU* 4.0 14.4 - - + -
122A LEU* 4.2 14.6 - - + -
124A ALA* 3.9 36.3 - - + +
125A ASP 4.5 0.2 - - - +
126A LEU* 3.1 55.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE 2.8 22.7 + - - +
90A TRP* 4.0 2.9 - - - +
92A LEU* 1.3 73.6 - - - +
94A ASP* 1.3 58.0 + - - +
95A VAL* 2.8 18.6 + - - +
101A LEU* 4.8 2.7 - - + -
105A GLU* 3.9 20.4 - - - +
108A LEU* 4.1 11.3 - - - +
109A ALA* 3.5 38.1 - - + +
112A LEU* 4.2 6.3 - - + -
126A LEU* 5.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TRP* 2.8 39.0 + - + +
91A LYS* 4.3 1.4 - - - +
92A LEU 3.4 0.9 - - - -
93A ALA* 1.3 68.9 - - - +
95A VAL* 1.3 53.9 + - - +
97A LYS* 2.7 44.8 + - + +
98A ASP* 2.7 23.9 + - - +
99A GLY* 3.2 9.4 + - - -
100A LEU 2.7 7.8 - - - +
101A LEU* 3.5 10.3 - - + +
105A GLU* 2.7 4.2 - - - +
141A CA 1.7 35.6 - - - -
148B TYR* 4.8 2.4 - - - +
----------------------------------------------------------
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