Contacts of the helix formed by residues 113 - 127 (chain B) in PDB entry 1K7E
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 GLY 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B THR* 3.3 18.0 + - - -
111B GLY 3.3 1.4 - - - -
112B ALA* 1.3 79.1 - - - +
114B GLN* 1.3 55.1 + - - +
116B GLY* 3.0 3.1 + - - -
117B VAL* 2.7 38.2 + - - +
134B MET* 3.8 12.8 - - - -
145B ASN* 3.6 20.0 - - - -
149B MET* 3.8 2.3 - - - +
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Residues in contact with GLN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLY* 3.1 33.0 + - - +
85B ALA* 4.0 16.9 + - + +
87B LYS* 3.6 20.2 - - + +
88B THR* 5.4 1.2 + - - -
112B ALA* 3.4 6.8 + - + -
113B GLY* 1.3 79.4 - - - +
115B HIS* 1.3 55.8 + - - +
117B VAL* 3.6 16.4 + - - +
118B ALA* 2.9 33.4 + - - +
121B LEU* 5.8 0.2 - - - +
145B ASN* 3.9 10.6 + - - +
382B LYS* 5.2 13.2 - - + +
402B PLP 3.9 18.2 - - + +
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Residues in contact with HIS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LYS* 3.4 26.4 - - + +
90B GLN* 3.6 9.4 + - - -
91B VAL* 3.6 22.6 - - + +
108B ALA* 3.9 4.3 - - + -
109B GLU* 3.0 24.2 - - - +
110B THR* 3.4 8.5 + - - +
113B GLY 3.3 0.6 - - - -
114B GLN* 1.3 74.9 - - - +
116B GLY* 1.3 54.2 + - - +
118B ALA* 3.4 1.0 + - - +
119B SER* 2.7 57.4 + - - -
187B MET* 2.9 28.5 + - + -
188B LEU 3.8 0.2 - - - -
189B GLY* 3.2 33.0 + - - +
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Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B THR* 3.0 19.9 + - - -
113B GLY 3.0 3.7 + - - -
115B HIS* 1.3 75.3 - - - +
117B VAL* 1.3 58.5 + - - +
119B SER* 3.2 1.2 + - - -
120B ALA* 2.8 26.9 + - - +
132B ILE* 3.0 33.9 - - - +
149B MET* 3.5 9.4 - - - -
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLY* 5.5 3.4 - - - +
113B GLY 2.7 23.3 + - - +
114B GLN* 3.7 19.3 - - - +
116B GLY* 1.3 70.1 - - - +
118B ALA* 1.3 63.2 + - - +
120B ALA* 3.3 3.1 + - - +
121B LEU* 2.9 33.6 + - + +
145B ASN* 3.8 27.8 - - + +
148B ARG* 4.2 26.2 - - + -
149B MET* 3.5 15.6 - - + +
152B MET* 4.2 8.3 - - + +
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LYS* 4.1 21.5 - - + -
88B THR* 4.4 9.6 - - - +
91B VAL* 3.6 24.8 - - + +
114B GLN* 2.9 26.3 + - - +
115B HIS* 3.8 3.8 - - - +
116B GLY 3.2 0.2 - - - -
117B VAL* 1.3 79.7 - - - +
119B SER* 1.3 61.7 + - - +
121B LEU* 3.3 13.1 + - - +
122B ALA 3.0 17.0 + - - -
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B VAL* 4.2 1.1 - - - -
106B ILE* 4.7 0.2 - - - -
108B ALA* 3.4 16.6 - - - +
115B HIS* 2.7 48.6 + - - -
116B GLY 3.9 3.1 - - - -
118B ALA* 1.3 70.4 - - - +
120B ALA* 1.4 66.1 + - - +
122B ALA* 3.2 2.5 + - - +
123B SER* 2.7 29.4 + - - -
130B CYS* 4.1 9.4 - - - -
132B ILE* 4.6 0.4 - - - -
187B MET* 3.4 24.8 - - - +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLY 2.8 17.8 + - - +
117B VAL* 3.7 4.3 - - - +
119B SER* 1.4 78.9 - - - +
121B LEU* 1.4 61.1 + - - +
123B SER* 3.1 2.4 + - - -
124B ALA* 3.0 25.1 + - - +
130B CYS* 4.1 10.3 - - - -
132B ILE* 4.4 0.4 - - + -
149B MET* 4.1 13.9 - - + -
152B MET* 4.1 17.6 - - + +
154B ALA* 3.9 24.7 - - + -
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TYR* 3.6 26.5 + - + +
82B HIS* 4.0 21.3 - - + +
83B GLY* 4.4 12.3 - - - -
88B THR* 4.3 21.3 - - + +
91B VAL* 5.3 0.9 - - + -
92B LEU* 5.3 1.8 - - + -
117B VAL* 2.9 24.8 + - + +
118B ALA* 3.3 19.3 - - + +
120B ALA* 1.4 71.1 - - - +
122B ALA* 1.3 75.9 + - + +
123B SER 3.0 2.0 + - - -
124B ALA* 4.1 5.4 - - - +
125B LEU* 3.3 20.6 + - - +
152B MET* 3.5 30.2 - - + -
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B VAL* 3.8 34.1 - - + +
92B LEU* 4.0 18.4 - - + -
95B ALA* 4.3 8.7 - - + -
118B ALA 3.0 16.8 + - - +
119B SER 4.0 3.4 - - - +
121B LEU* 1.3 84.3 - - + +
123B SER* 1.3 59.8 + - - +
125B LEU* 3.4 2.0 + - - +
126B LEU* 2.9 35.3 + - - +
187B MET* 4.6 4.0 - - + -
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ILE* 3.9 17.2 - - - +
119B SER 2.7 21.0 + - - -
120B ALA 3.4 5.2 - - - -
122B ALA* 1.3 78.9 - - - +
124B ALA* 1.3 61.4 + - - +
126B LEU 3.2 0.4 + - - +
127B GLY* 2.9 11.3 + - - -
128B LEU* 2.8 47.7 + - - +
130B CYS* 3.3 31.8 - - - +
152B MET 5.9 0.4 - - - -
187B MET* 5.0 1.6 - - - +
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ALA 3.0 12.2 + - - +
121B LEU* 4.1 6.1 - - - +
123B SER* 1.3 79.8 - - - +
125B LEU* 1.3 67.2 + - - +
126B LEU 3.2 0.5 + - - -
127B GLY* 3.4 7.1 + - - -
128B LEU 5.0 1.3 - - - -
152B MET* 3.6 25.6 - - + +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 3.7 29.6 - - + -
52B TYR* 3.7 48.0 - - + +
92B LEU* 4.3 7.4 - - + -
121B LEU 3.3 11.3 + - - +
122B ALA 3.5 7.0 - - - +
123B SER 3.2 0.2 - - - -
124B ALA* 1.3 82.3 - - - +
126B LEU* 1.3 76.3 + - + +
127B GLY 3.6 0.3 + - - -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLN* 5.4 4.0 - - - +
48B LEU* 4.3 17.5 - - + -
92B LEU* 4.1 7.2 - - + +
95B ALA* 3.4 31.0 - - + -
96B LEU* 3.8 28.3 - - + -
99B LYS* 2.7 42.5 + - + +
122B ALA 2.9 17.8 + - - +
124B ALA 3.1 0.2 - - - -
125B LEU* 1.3 101.1 - - + +
127B GLY* 1.3 61.8 + - - +
128B LEU* 3.4 7.9 + - + +
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LYS* 4.7 2.9 + - - -
104B SER* 4.4 3.5 - - - +
123B SER 2.9 4.2 + - - -
124B ALA 3.4 8.7 + - - -
125B LEU 3.4 0.6 + - - -
126B LEU* 1.3 78.9 - - - +
128B LEU* 1.4 63.8 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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