Contacts of the helix formed by residues 108 - 119 (chain K) in PDB entry 5T0G
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 THR 108 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73K HIS* 4.8 2.0 - - - -
74K ILE* 3.7 0.9 - - - -
99K HIS* 5.3 1.5 - - + -
106K THR 4.7 2.2 - - - +
107K MET* 1.3 77.0 - - - +
109K VAL* 1.3 62.8 + - - +
110K GLU* 3.7 8.2 + - - +
111K SER* 2.2 49.4 + - - -
112K VAL* 3.5 9.2 - - - +
147K ASP* 4.4 7.4 - - - +
148K GLU* 3.2 37.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73K HIS* 4.9 0.2 - - - +
74K ILE* 3.8 14.3 - - + +
108K THR* 1.3 75.0 - - - +
110K GLU* 1.3 62.0 + - - +
111K SER 3.4 0.5 + - - -
112K VAL* 3.5 15.0 + - - +
113K THR* 3.9 2.6 + - - -
143K PHE* 4.5 8.6 - - + +
144K GLY 4.2 21.5 - - - +
145K GLY* 3.5 21.5 - - - +
146K VAL 3.5 3.1 - - - +
147K ASP* 3.4 36.8 - - + +
152K GLN* 4.3 11.7 - - + +
154K PHE* 3.6 29.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108K THR* 3.2 8.6 + - - +
109K VAL* 1.3 78.9 - - - +
111K SER* 1.3 62.4 + - - +
113K THR* 3.1 13.2 + - - -
114K GLN* 2.8 34.5 + - - +
147K ASP* 5.3 5.7 + - - +
149K LYS* 4.9 11.7 + - - -
154K PHE* 3.5 23.7 - - + -
162K PHE* 5.2 11.7 - - + -
61L LYS* 4.5 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K HIS* 6.0 0.7 - - - -
107K MET* 2.8 39.4 - - - +
108K THR* 2.2 45.8 + - - -
110K GLU* 1.3 72.5 - - - +
112K VAL* 1.3 63.6 + - - +
113K THR 3.1 0.3 + - - -
114K GLN* 3.3 8.1 + - - +
115K ALA* 2.9 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70K ILE* 5.3 6.5 - - + -
74K ILE* 3.9 29.2 - - + -
92K ALA* 5.0 13.0 - - + -
95K GLU* 5.7 0.2 - - - +
96K THR* 4.3 17.9 - - + -
107K MET* 5.0 1.1 - - - -
108K THR 3.5 15.9 - - - +
109K VAL 3.7 9.0 - - - +
110K GLU 3.3 0.4 - - - -
111K SER* 1.3 76.3 + - - +
113K THR* 1.3 63.1 + - - +
115K ALA* 3.3 10.0 + - + +
116K VAL* 2.9 28.8 + - + +
143K PHE* 3.8 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 113 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109K VAL 3.9 0.4 + - - -
110K GLU* 3.1 15.0 + - - -
111K SER 3.1 1.0 - - - -
112K VAL* 1.3 80.2 - - - +
114K GLN* 1.3 65.0 + - - +
116K VAL* 3.0 2.6 + - - +
117K SER* 2.6 39.6 + - - +
143K PHE* 3.9 20.3 - - + -
154K PHE* 3.9 8.8 - - - -
156K MET* 5.1 4.0 - - + +
162K PHE* 3.3 60.2 - - + -
82L ARG* 5.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110K GLU* 2.8 42.7 + - - +
111K SER* 3.3 6.2 + - - +
113K THR* 1.3 84.1 - - - +
115K ALA* 1.3 61.9 + - - +
117K SER* 3.7 8.7 - - - +
118K ASN* 2.9 39.1 + - - +
162K PHE* 5.2 5.3 - - - -
61L LYS* 5.4 6.3 - - - +
82L ARG* 5.2 16.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
95K GLU* 3.2 32.1 - - + +
96K THR* 6.2 0.7 - - + -
107K MET* 5.0 10.1 - - + -
111K SER 2.9 15.0 + - - +
112K VAL* 3.3 16.4 - - + +
114K GLN* 1.3 79.3 - - - +
116K VAL* 1.3 60.7 + - + +
118K ASN* 3.9 10.5 + - - +
119K LEU* 3.5 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88K LEU* 4.6 10.3 - - + -
92K ALA* 4.8 14.1 - - + -
95K GLU* 4.8 1.6 - - - +
112K VAL* 2.9 21.6 + - + +
113K THR 3.8 2.7 - - - +
115K ALA* 1.3 77.7 - - + +
117K SER* 1.3 60.3 + - - +
119K LEU* 3.2 24.2 - - + +
120K ALA* 2.9 25.6 + - - +
141K LEU* 4.1 13.9 - - + -
143K PHE* 3.6 18.4 - - + -
156K MET* 3.5 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113K THR* 2.6 33.0 + - - +
114K GLN* 3.2 9.2 + - - -
116K VAL* 1.3 75.2 - - - +
118K ASN* 1.3 67.1 + - - +
120K ALA* 3.0 24.1 + - - +
121K LEU 4.7 0.2 + - - -
156K MET* 4.8 8.3 - - - +
160K GLY 4.1 3.2 + - - -
162K PHE* 5.0 0.7 - - - +
79L ALA* 5.5 3.8 - - - +
82L ARG* 3.1 44.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 118 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114K GLN* 2.9 30.2 + - - +
115K ALA* 4.1 7.2 - - - +
116K VAL 3.3 0.2 - - - -
117K SER* 1.3 79.1 - - - +
119K LEU* 1.3 58.5 + - + +
120K ALA 3.5 0.3 + - - -
121K LEU 4.9 3.5 + - - +
122K GLN* 4.4 9.2 + - - +
82L ARG* 5.1 7.4 - - - +
83L LEU* 5.6 3.1 + - - +
86L ASN* 3.6 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88K LEU* 3.7 33.4 - - + +
91K LYS* 3.3 35.9 - - + +
92K ALA* 6.1 0.7 - - + +
95K GLU* 3.4 17.7 - - - +
115K ALA 3.5 9.0 - - - +
116K VAL* 3.2 37.2 - - + +
118K ASN* 1.3 76.3 - - - +
120K ALA* 1.3 67.3 + - - +
121K LEU 3.5 1.7 + - - -
122K GLN* 3.7 34.2 + - - +
----------------------------------------------------------
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