Contacts of the helix formed by residues 99 - 109 (chain A) in PDB entry 3KCC
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 TYR 99 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 3.4 20.5 - - - +
37A GLU* 2.9 24.8 + - - +
38A THR 3.4 26.7 - - - -
39A LEU* 3.7 12.3 - - + -
71A GLY 2.5 25.3 + - - -
74A GLY* 3.2 39.0 + - - -
75A LEU* 3.4 33.4 - - + -
82A ARG* 3.3 9.0 + - - -
97A ILE 3.6 0.2 + - - -
98A SER* 1.3 71.6 - - - +
100A LYS* 1.3 63.5 + - - +
102A PHE* 3.3 2.5 + - + +
103A ARG* 2.9 52.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A SER* 3.1 10.1 + - - +
99A TYR* 1.3 80.8 - - - +
101A LYS* 1.3 62.3 + - - +
103A ARG* 3.4 19.7 + - - +
104A GLN* 3.4 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A HIS* 2.8 56.4 + - + +
97A ILE* 3.7 17.0 - - + -
98A SER* 3.0 19.2 + - - +
100A LYS* 1.3 75.3 - - - +
102A PHE* 1.3 66.6 + - - +
104A GLN* 3.0 29.3 + - - +
105A LEU* 3.1 16.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.6 32.5 - + - -
39A LEU* 3.6 23.3 - - + -
69A PHE* 4.6 3.1 - + - -
75A LEU* 3.7 30.1 - - + -
97A ILE* 4.0 13.2 - - + +
98A SER 2.9 17.8 + - - +
99A TYR* 3.7 7.4 - - - +
101A LYS* 1.3 76.2 - - - +
103A ARG* 1.3 57.2 + - - +
105A LEU* 3.1 10.0 + - + +
106A ILE* 3.0 46.8 + - + +
112A ILE* 3.8 38.4 - - + -
113A LEU* 4.9 1.3 - - + -
116A LEU* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLY 5.3 0.2 + - - -
75A LEU* 3.0 39.8 + - + -
76A PHE 5.7 0.4 - - - -
77A GLU 6.1 2.0 - - - -
78A GLU* 6.1 0.6 - - - +
99A TYR* 2.9 38.9 + - - +
100A LYS* 3.7 26.2 - - - +
101A LYS 3.2 0.2 - - - -
102A PHE* 1.3 77.7 - - - +
104A GLN* 1.3 61.1 + - + +
106A ILE* 3.3 13.3 + - + +
107A GLN* 3.3 24.1 + - - +
114B MET* 4.5 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS* 3.4 35.1 + - - +
101A LYS* 3.0 23.9 + - - +
103A ARG* 1.3 75.8 - - + +
105A LEU* 1.3 67.4 + - + +
107A GLN* 3.1 11.8 + - - +
108A VAL* 3.1 26.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TRP* 3.3 31.8 - - + -
14A PHE* 3.9 26.9 - - + -
17A HIS* 3.6 41.1 - - + +
97A ILE* 3.7 26.2 - - + -
101A LYS* 3.1 19.8 + - + +
102A PHE* 3.4 10.1 - - + +
104A GLN* 1.3 79.1 - - + +
106A ILE* 1.3 56.6 + - - +
108A VAL* 3.1 4.8 + - + -
109A ASN 2.8 28.2 + - - +
112A ILE* 4.4 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.6 2.2 - - + -
102A PHE* 3.0 47.4 + - + +
103A ARG* 3.5 15.7 - - + +
104A GLN 3.2 0.4 - - - -
105A LEU* 1.3 75.5 - - - +
107A GLN* 1.3 65.6 + - - +
109A ASN 4.1 6.1 - - - -
110A PRO* 3.1 27.6 - - + +
112A ILE* 4.3 5.6 - - + -
113A LEU* 3.9 33.0 - - + -
110B PRO* 3.9 24.4 - - + +
114B MET* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG 3.3 12.1 + - - +
104A GLN* 3.1 12.2 + - - +
106A ILE* 1.3 82.3 - - - +
108A VAL* 1.3 65.0 + - + +
110A PRO* 4.4 5.0 - - - +
109B ASN* 5.4 1.6 + - - -
110B PRO* 4.0 28.6 - - - +
111B ASP* 5.2 4.4 - - - +
114B MET* 6.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TRP* 3.7 25.6 - - + +
104A GLN* 3.1 16.9 + - + +
105A LEU* 3.1 8.9 + - + +
107A GLN* 1.3 78.7 - - + +
109A ASN* 1.3 62.1 + - + +
110A PRO* 4.2 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 4.2 18.6 + - - +
13A TRP* 3.7 24.6 - - + -
105A LEU 2.8 9.8 + - - +
106A ILE 3.3 2.2 - - - -
108A VAL* 1.3 79.5 - - + +
110A PRO* 1.3 63.6 - - - +
111A ASP* 2.9 41.3 + - - +
112A ILE* 3.2 22.9 + - - +
107B GLN* 5.1 1.0 - - - +
----------------------------------------------------------
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