Contacts of the helix formed by residues 94 - 107 (chain E) in PDB entry 1KQN
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 GLU 94 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92E TRP* 3.6 18.0 - - + +
93E LYS* 1.3 73.5 - - - +
95E THR* 1.3 66.7 + - - +
96E LEU* 4.2 3.8 - - + +
97E LYS* 3.0 50.7 + - + +
98E VAL* 3.2 7.8 + - - +
170E LYS* 4.8 13.4 + - + -
173E ASP* 3.7 22.0 - - - +
272E ARG* 2.7 45.2 + - - -
273E ASN* 4.9 5.4 - - - +
781E NAD 3.4 12.1 - - - +
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Residues in contact with THR 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E CYS* 4.2 19.8 - - + +
86E GLU* 5.7 0.3 + - - -
93E LYS 3.4 2.4 + - - -
94E GLU* 1.3 72.0 - - - +
96E LEU* 1.3 62.1 + - - +
98E VAL* 3.1 10.9 + - - +
99E LEU* 2.9 29.5 + - + +
153E LEU* 3.8 30.7 - - + -
159E LEU* 5.8 0.8 - - + +
169E TRP* 3.9 11.6 - - + -
177E ILE* 4.5 1.3 - - + -
781E NAD 2.7 53.1 + - - -
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Residues in contact with LEU 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E GLU* 3.1 2.9 + - + +
95E THR* 1.3 78.5 - - - +
97E LYS* 1.3 59.7 + - + +
99E LEU* 3.3 3.8 + - + +
100E ARG* 2.9 44.6 + - - +
173E ASP* 3.5 38.8 - - + +
176E GLN* 3.8 39.3 - - + +
177E ILE* 4.1 27.0 - - + +
181E TYR* 3.6 30.3 - - + +
781E NAD 4.3 1.0 + - - -
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Residues in contact with LYS 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E TRP* 4.7 3.9 - - + -
93E LYS* 4.5 29.8 - - + +
94E GLU* 3.0 47.8 + - + +
96E LEU* 1.3 75.0 - - + +
98E VAL* 1.3 60.5 + - - +
100E ARG* 3.2 28.2 + - - +
101E HIS* 2.7 32.8 + - - +
170E LYS* 5.6 7.4 - - - +
272E ARG* 4.5 4.4 - - - +
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Residues in contact with VAL 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E LEU* 4.0 3.1 - - + -
14E CYS* 3.6 17.3 - - - -
49E SER* 4.0 6.3 - - - +
85E TRP* 4.0 11.0 - - + -
86E GLU* 3.4 47.8 - - + +
93E LYS* 3.9 12.6 - - + +
94E GLU 3.4 14.1 - - - +
95E THR* 3.1 9.4 + - - +
97E LYS* 1.3 76.9 - - - +
99E LEU* 1.3 63.3 + - - +
101E HIS* 3.4 0.9 + - - +
102E HIS* 3.0 46.4 + - + +
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Residues in contact with LEU 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E LEU* 3.8 16.8 - - + -
95E THR* 2.9 26.4 + - + +
96E LEU* 3.5 7.6 - - - +
98E VAL* 1.3 76.1 - - - +
100E ARG* 1.3 63.4 + - - +
102E HIS* 3.1 4.9 + - - +
103E GLN* 2.9 22.0 + - - +
151E VAL* 3.7 28.0 - - + +
152E LYS 4.3 0.2 - - - -
153E LEU* 4.0 30.1 - - + +
177E ILE* 3.9 35.0 - - + -
181E TYR* 4.0 29.5 - - + -
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Residues in contact with ARG 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E LEU* 2.9 41.7 + - - +
97E LYS* 3.5 35.3 - - - +
99E LEU* 1.3 75.4 - - - +
101E HIS* 1.3 55.7 + - - +
103E GLN* 2.7 23.4 + - + -
104E GLU* 2.8 45.1 + - + +
176E GLN* 4.2 10.3 + - - +
181E TYR* 3.3 22.9 + - - +
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Residues in contact with HIS 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E TRP* 3.1 73.0 - + + +
97E LYS 2.7 21.6 + - - +
98E VAL 3.5 4.7 - - - +
100E ARG* 1.3 73.3 - - - +
102E HIS* 1.3 77.1 + + - +
104E GLU* 3.6 9.0 + - - +
105E LYS* 3.0 46.1 + - + +
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Residues in contact with HIS 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E LEU* 4.1 20.4 - - + +
47E ILE* 3.8 22.8 - - + +
49E SER* 4.9 3.2 + - - -
83E ASP* 2.9 46.7 + - + +
85E TRP* 4.8 4.2 - + - +
86E GLU 5.7 0.6 + - - -
98E VAL* 3.0 43.7 + - + +
99E LEU 3.7 4.5 - - - +
100E ARG 3.1 0.4 - - - -
101E HIS* 1.3 93.0 - + - +
103E GLN* 1.3 60.1 + - - +
105E LYS* 3.8 15.9 + - - +
106E LEU* 3.4 26.9 + - - +
151E VAL* 3.8 12.0 - - + +
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Residues in contact with GLN 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E LEU 2.9 10.4 + - - +
100E ARG* 2.7 14.9 + - + +
102E HIS* 1.3 69.4 - - - +
104E GLU* 1.3 68.1 + - + +
105E LYS 3.1 1.3 - - - -
106E LEU* 3.0 13.6 + - - +
107E GLU* 3.2 30.8 + - - +
148E VAL* 3.9 12.7 - - - +
149E PRO 3.1 22.8 + - - -
150E LYS* 3.7 6.6 - - - +
151E VAL* 2.9 35.1 + - + +
180E ASN 5.7 0.3 - - - +
181E TYR* 3.9 21.1 - - + +
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Residues in contact with GLU 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E ARG* 2.8 44.4 + - + +
101E HIS* 4.0 8.3 - - - +
103E GLN* 1.3 75.7 - - + +
105E LYS* 1.3 58.4 + - - +
107E GLU* 2.9 43.1 + - - +
108E ALA* 4.5 1.9 - - - +
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Residues in contact with LYS 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E LYS* 5.8 6.2 - - - +
47E ILE* 6.1 0.4 - - - +
81E GLU* 5.7 2.0 + - - -
83E ASP* 3.2 26.9 + - - -
85E TRP* 6.1 0.4 - - - +
101E HIS* 3.0 35.8 + - + +
102E HIS* 3.8 17.0 + - - +
104E GLU* 1.3 77.6 - - - +
106E LEU* 1.3 63.2 + - + +
107E GLU 3.4 0.5 + - - -
108E ALA* 3.7 18.7 + - - +
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Residues in contact with LEU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E VAL* 3.6 30.5 - - + -
45E LYS* 4.8 17.5 - - - +
47E ILE* 6.2 1.3 - - + -
102E HIS 3.4 9.1 + - - +
103E GLN* 3.0 9.8 + - - +
105E LYS* 1.3 80.5 - - + +
107E GLU* 1.3 56.8 + - - +
108E ALA 3.0 12.7 + - - +
148E VAL* 4.0 20.0 - - + +
149E PRO* 3.4 32.9 - - + +
151E VAL* 3.6 20.0 - - + -
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Residues in contact with GLU 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E GLN* 3.2 29.2 + - - +
104E GLU* 2.9 24.3 + - - +
106E LEU* 1.3 75.1 - - - +
108E ALA* 1.3 62.4 + - - +
148E VAL* 4.0 28.8 - - + +
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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
------------------------------------------------------------
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