Contacts of the helix formed by residues 115 - 130 (chain K) in PDB entry 6D84
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 115 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K PHE* 5.8 0.2 - - - -
113K HIS* 3.1 23.9 + - - -
114K SER* 1.3 77.7 - - - +
116K GLN* 1.3 63.1 + - + +
117K PHE* 3.4 24.2 - - + +
118K VAL* 3.9 9.3 - - + +
119K GLN* 3.0 31.6 + - - +
141Q LEU* 3.8 30.5 - - + +
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Residues in contact with GLN 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K SER 3.7 3.4 + - - -
115K THR* 1.3 73.3 - - + +
117K PHE* 1.3 83.1 + - + +
119K GLN* 4.2 2.5 - - - -
120K GLY* 2.6 26.7 + - - -
150K ASN* 2.5 49.4 + - - +
152K TYR* 3.2 37.6 - - + +
153K LEU* 3.3 16.9 - - + +
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Residues in contact with PHE 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K PHE* 3.9 19.1 - - + -
83K ARG* 4.7 3.6 + - - +
115K THR* 3.2 17.6 - - + -
116K GLN* 1.3 106.1 - - + +
118K VAL* 1.3 60.9 + - - +
120K GLY* 3.4 1.1 - - - +
121K LEU* 2.9 32.7 + - - +
152K TYR* 3.2 40.0 + + - -
116Q GLU* 5.4 0.9 - - - +
134Q ALA* 3.2 31.0 - - + -
137Q ASP* 3.8 22.7 - - + -
138Q SER* 3.7 18.6 - - - -
141Q LEU* 4.6 9.0 - - + -
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Residues in contact with VAL 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K PHE* 3.6 30.3 - - + -
82K LYS* 4.1 17.3 - - + -
86K TYR* 4.8 3.9 - - + -
110K ASP* 3.8 20.5 - - - +
113K HIS* 3.4 52.7 - - + +
115K THR* 3.4 6.7 + - - -
117K PHE* 1.3 73.2 - - - +
119K GLN* 1.3 59.6 + - - +
121K LEU* 3.2 10.0 + - + +
122K ALA* 2.9 27.2 + - - +
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Residues in contact with GLN 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110K ASP 3.3 19.3 - - - +
111K LEU* 2.7 30.3 + - + +
112K ASN* 3.8 3.6 - - - +
113K HIS 2.4 29.8 + - - +
114K SER 5.0 1.8 - - - -
115K THR 3.0 16.1 + - - +
116K GLN* 3.5 0.9 - - - -
118K VAL* 1.3 74.6 - - - +
120K GLY* 1.3 57.7 + - - +
122K ALA* 3.8 2.3 - - - +
123K LEU* 2.9 33.8 + - - +
145K LEU* 3.3 13.9 - - + +
153K LEU* 3.3 34.8 - - + +
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Residues in contact with GLY 120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116K GLN 2.6 22.2 + - - -
117K PHE 3.2 4.8 + - - -
119K GLN* 1.3 75.3 - - - +
121K LEU* 1.3 57.8 + - - +
123K LEU 3.5 0.3 + - - -
124K CYS* 2.8 29.2 + - - +
152K TYR* 4.3 2.2 - - - -
153K LEU* 4.4 2.0 - - - -
156K LYS* 3.6 33.6 - - - +
116Q GLU* 4.9 2.7 - - - -
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Residues in contact with LEU 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K PHE* 5.0 5.4 - - + +
82K LYS* 4.4 3.6 - - + -
83K ARG* 3.3 63.5 - - + +
86K TYR* 3.6 31.1 - - + -
90K MET* 5.7 3.4 - - + -
117K PHE 2.9 19.0 + - - +
118K VAL* 3.2 12.5 + - + +
120K GLY* 1.3 74.2 - - - +
122K ALA* 1.3 60.8 + - - +
124K CYS* 3.5 11.8 - - + +
125K THR* 2.9 35.7 + - - -
112Q PHE* 5.9 0.7 - - + -
115Q ASP* 5.8 5.4 - - + +
116Q GLU* 4.7 10.3 - - - +
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Residues in contact with ALA 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K TYR* 4.1 8.4 - - - +
107K ILE* 3.4 25.1 - - + +
110K ASP* 3.6 31.2 - - + +
111K LEU* 3.7 14.4 - - + -
118K VAL 2.9 17.0 + - - +
119K GLN 3.8 0.9 - - - +
120K GLY 3.4 0.2 - - - -
121K LEU* 1.3 75.8 - - - +
123K LEU* 1.3 60.4 + - - +
126K LEU* 3.3 23.2 + - - +
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Residues in contact with LEU 123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111K LEU* 3.8 18.6 - - + -
119K GLN 2.9 19.9 + - - +
120K GLY 3.8 3.8 - - - +
122K ALA* 1.3 75.6 - - - +
124K CYS* 1.3 59.4 + - - +
126K LEU* 3.8 2.5 - - + +
127K GLY* 2.9 27.5 + - - -
142K VAL* 4.8 10.1 - - + -
145K LEU* 4.5 14.4 - - + -
153K LEU* 3.8 27.6 - - + +
156K LYS* 3.7 31.6 - - + +
157K ALA* 3.9 12.6 - - + +
160K CYS* 4.0 30.9 - - + +
119Q ILE* 4.4 3.8 - - - +
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Residues in contact with CYS 124 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90K MET* 3.6 24.5 - - - -
120K GLY 2.8 18.7 + - - +
121K LEU* 3.1 15.2 + - + +
123K LEU* 1.3 76.5 - - - +
125K THR* 1.3 57.7 + - - +
127K GLY* 3.3 1.2 + - - -
128K CYS* 2.9 35.4 + - - -
156K LYS* 5.2 4.2 - - - +
115Q ASP* 3.6 30.3 - - - +
116Q GLU* 5.4 1.3 - - - +
119Q ILE* 3.6 27.4 - - + +
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Residues in contact with THR 125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86K TYR* 3.1 42.2 + - + +
89K ALA* 3.8 18.6 - - + -
90K MET* 3.6 21.8 - - + +
103K MET* 4.4 7.2 - - - -
107K ILE* 4.5 5.6 - - + -
121K LEU 2.9 9.9 + - - -
122K ALA 4.8 0.2 - - - -
124K CYS* 1.3 75.9 - - - +
126K LEU* 1.3 58.7 + - - +
129K MET* 2.9 51.2 + - - +
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Residues in contact with LEU 126 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K ILE* 4.6 8.9 - - + +
111K LEU* 4.6 7.4 - - + -
122K ALA 3.3 20.5 + - - +
123K LEU* 4.0 3.8 - - + +
124K CYS 3.3 0.6 - - - -
125K THR* 1.3 80.1 - - - +
127K GLY* 1.3 55.2 + - - +
130K GLY* 3.0 37.0 + - - +
134K MET* 4.4 23.1 - - + +
135K CYS* 5.0 4.9 - - - +
138K LEU* 3.7 39.9 - - + -
142K VAL* 3.7 22.4 - - + -
160K CYS* 3.7 9.6 - - - -
163K HIS* 3.1 14.6 - - - -
164K VAL* 5.3 3.8 - - + -
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Residues in contact with GLY 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K LEU 2.9 18.5 + - - -
124K CYS 3.3 1.3 + - - -
126K LEU* 1.3 76.1 - - - +
128K CYS* 1.3 59.6 + - - +
160K CYS* 4.3 5.8 - - - -
163K HIS* 2.8 35.5 + - - +
119Q ILE* 4.0 13.0 - - - -
120Q GLY* 3.5 19.8 - - - -
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Residues in contact with CYS 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90K MET* 3.8 28.9 - - + -
124K CYS* 2.9 24.2 + - - +
125K THR 4.1 0.9 - - - +
127K GLY* 1.3 79.8 - - - +
129K MET* 1.3 62.1 + - + +
130K GLY 3.9 0.4 - - - -
163K HIS* 4.0 6.3 - - - -
167K LYS* 5.2 0.5 + - - -
18Q LYS* 4.2 16.8 - - - +
19Q TRP 4.6 10.7 - - - +
20Q TYR* 4.2 21.5 - - + +
22Q THR* 5.4 2.9 - - - +
115Q ASP* 4.8 1.3 - - - -
118Q ILE 4.6 2.5 - - - -
119Q ILE* 4.0 27.6 - - - -
120Q GLY* 4.0 6.0 - - - +
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Residues in contact with MET 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89K ALA 3.6 15.3 - - - +
90K MET* 3.9 17.0 - - + +
93K LEU* 3.4 41.5 - - + +
94K ASP* 3.8 15.5 - - + +
95K GLU* 4.9 2.8 - - - +
100K HIS* 4.7 1.7 + - + +
103K MET* 3.7 21.8 - - + -
107K ILE* 6.1 0.2 - - - -
125K THR* 2.9 35.3 + - + +
126K LEU* 5.6 0.2 - - - -
128K CYS* 1.3 79.9 - - + +
130K GLY* 1.3 66.5 + - - +
131K SER* 3.2 4.7 + - - -
134K MET* 5.1 1.3 - - - +
163K HIS* 4.1 3.1 - - - -
167K LYS* 4.8 1.8 - - - -
19Q TRP 5.8 2.0 - - - +
22Q THR* 4.8 16.6 - - + -
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Residues in contact with GLY 130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125K THR 3.6 1.4 + - - -
126K LEU* 3.0 40.1 + - - -
129K MET* 1.3 76.0 - - - +
131K SER* 1.3 67.8 + - - +
134K MET* 4.6 6.1 - - - -
135K CYS* 3.6 1.0 - - - -
163K HIS* 2.5 26.2 + - - -
167K LYS* 3.6 7.9 + - - +
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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) + - + + + + + -
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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