Contacts of the helix formed by residues 100 - 116 (chain K) in PDB entry 6C0W
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 ASP 100 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K PHE* 1.3 101.3 - - - +
101K MET* 1.3 62.2 + - - +
102K LYS* 4.3 7.5 - - + +
103K GLN* 3.0 51.6 + - - +
104K PHE 4.0 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 101 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K PHE* 4.7 8.7 - - - +
100K ASP* 1.3 76.2 - - - +
102K LYS* 1.3 60.0 + - - +
103K GLN 3.4 0.9 - - - -
104K PHE* 3.4 29.4 - - + +
105K LYS* 2.9 43.9 + - + +
129K ASN* 5.2 7.2 - - + +
131K VAL* 3.8 33.0 - - + -
154K TYR* 3.8 13.9 - - + -
156K SER* 3.7 32.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100K ASP* 3.5 7.9 - - + +
101K MET* 1.3 75.1 - - - +
103K GLN* 1.3 63.1 + - + +
105K LYS* 3.2 12.4 + - + +
106K ASN* 2.9 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K PHE* 4.8 9.4 - - + -
100K ASP* 3.0 37.3 + - - +
102K LYS* 1.3 78.0 - - + +
104K PHE* 1.3 56.5 + - - +
106K ASN* 3.9 6.8 - - - +
107K SER* 2.8 37.9 + - - +
184K LYS* 5.0 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 104 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K PHE* 3.8 30.0 - + + -
100K ASP 4.0 1.6 + - - -
101K MET* 3.3 31.5 + - + +
102K LYS 3.2 0.6 - - - -
103K GLN* 1.3 76.5 - - - +
105K LYS* 1.3 64.5 + - + +
107K SER* 3.9 3.3 - - - -
108K PHE* 2.9 39.1 + + + +
123K PHE* 5.4 1.8 - + - -
131K VAL* 5.1 0.7 - - + -
133K ILE* 4.4 19.1 - - + -
154K TYR* 3.7 33.7 - + - -
179K LEU* 4.6 16.8 - - + -
182K ALA* 3.5 20.9 - - + -
183K SER* 3.7 31.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 105 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101K MET* 2.9 28.6 + - + +
102K LYS* 3.2 12.3 + - + +
104K PHE* 1.3 79.5 - - + +
106K ASN* 1.3 57.5 + - - +
109K LYS* 3.0 32.1 + - - +
123K PHE* 3.7 61.7 - - + +
125K GLU* 2.3 39.2 + - - +
131K VAL* 4.6 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 106 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102K LYS* 2.9 41.6 + - - +
103K GLN* 3.9 6.6 + - - +
105K LYS* 1.3 76.4 - - - +
107K SER* 1.3 58.1 + - - +
109K LYS* 3.4 6.6 + - - +
110K LYS* 3.0 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 107 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103K GLN* 2.8 26.5 + - - +
104K PHE 3.9 2.7 - - - -
106K ASN* 1.3 77.2 - - - +
108K PHE* 1.3 59.2 + - - +
110K LYS* 4.0 3.0 - - - +
111K ILE* 2.9 42.6 + - - +
182K ALA* 4.0 20.4 - - - -
184K LYS* 6.1 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 108 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K PHE* 2.9 28.0 + + + +
105K LYS* 4.0 3.6 - - - +
107K SER* 1.3 75.8 - - - +
109K LYS* 1.3 59.5 + - - +
111K ILE* 4.0 1.4 - - + +
112K LEU* 3.0 48.1 + - + +
121K VAL* 4.3 19.3 - - + -
123K PHE* 4.3 9.2 - + + -
133K ILE* 4.1 23.3 - - + -
135K ILE* 4.4 8.1 - - + -
152K VAL* 6.2 0.2 - - + -
175K LEU* 3.6 31.9 - - + -
178K ALA* 4.2 7.2 - - + -
179K LEU* 4.0 29.6 - - + -
182K ALA* 3.7 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 109 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105K LYS 3.0 18.2 + - - +
106K ASN* 4.0 7.0 - - - +
108K PHE* 1.3 80.3 - - - +
110K LYS* 1.3 64.4 + - + +
112K LEU* 4.0 2.6 - - - +
113K GLN* 2.9 65.2 + - + +
121K VAL* 4.6 30.7 + - + +
123K PHE* 5.0 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106K ASN* 3.0 31.8 + - + +
107K SER* 4.1 3.6 - - - +
109K LYS* 1.3 80.9 - - + +
111K ILE* 1.3 61.1 + - + +
113K GLN* 3.5 14.1 + - + +
114K ARG* 2.9 52.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K SER* 2.9 26.7 + - - +
108K PHE* 4.0 3.1 - - - +
110K LYS* 1.3 77.6 - - + +
112K LEU* 1.3 57.7 + - - +
114K ARG* 3.3 7.8 + - - +
115K ALA* 2.9 27.4 + - + +
178K ALA* 3.8 32.1 - - + +
181K ILE* 3.8 26.2 - - + +
182K ALA* 3.8 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108K PHE* 3.0 35.1 + - + +
109K LYS* 4.0 4.0 - - - +
111K ILE* 1.3 78.2 - - - +
113K GLN* 1.3 60.9 + - - +
115K ALA* 3.2 12.0 + - + +
116K LEU* 3.3 12.6 + - + +
119K VAL* 3.8 25.2 - - + +
121K VAL* 3.7 25.8 - - + -
135K ILE* 4.1 18.6 - - + -
137K TRP* 3.7 28.9 - - + -
174K LEU* 4.2 14.4 - - + -
175K LEU* 5.0 2.9 - - + -
178K ALA* 4.9 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 113 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109K LYS* 2.9 54.7 + - + +
110K LYS* 4.1 14.8 - - + +
112K LEU* 1.3 76.1 - - - +
114K ARG* 1.3 58.7 + - + +
115K ALA 3.4 0.2 - - - -
116K LEU 2.9 18.3 - - - +
117K LYS* 4.5 7.3 - - - +
119K VAL* 3.8 26.1 + - + +
120K THR* 6.3 0.2 - - - +
121K VAL* 5.5 3.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110K LYS* 2.9 37.4 + - + +
111K ILE* 3.8 7.4 - - - +
112K LEU 3.2 0.2 - - - -
113K GLN* 1.3 77.2 - - - +
115K ALA* 1.3 66.2 + - - +
116K LEU 4.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111K ILE* 2.9 19.3 + - + +
112K LEU* 3.2 10.1 + - + +
114K ARG* 1.3 81.3 - - - +
116K LEU* 1.3 67.7 + - - +
174K LEU* 4.0 33.7 - - + -
178K ALA* 5.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112K LEU* 3.3 5.8 + - + +
113K GLN* 2.9 25.8 - - - +
114K ARG 4.9 0.7 - - - -
115K ALA* 1.3 87.9 - - + +
117K LYS* 1.3 65.0 + - - +
118K ASN 4.5 3.6 - - - +
119K VAL* 4.4 15.2 - - + +
137K TRP* 4.5 16.6 - - + -
138K GLY 3.7 23.1 - - - +
139K THR* 5.5 2.5 - - - +
140K GLN* 5.4 11.0 - - + +
171K ASN* 4.1 21.5 - - - +
174K LEU* 5.2 7.0 - - + -
----------------------------------------------------------
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