Contacts of the helix formed by residues 91 - 104 (chain E) in PDB entry 2Q9Q
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 TYR 91 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E VAL* 4.0 7.2 - - + -
9E LEU* 3.9 28.2 + - + +
10E ALA* 3.4 35.4 - - + -
13E GLU* 3.5 28.0 - - - -
89E SER* 2.9 8.5 + - - +
90E PRO* 1.3 102.8 - - + +
92E TYR* 1.3 58.4 + - - +
94E GLU* 3.1 32.9 + - - +
95E LEU* 2.9 33.1 + - + +
149E THR* 4.8 0.7 - - - -
150E LEU* 4.2 20.4 - - + +
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Residues in contact with TYR 92 (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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65E TRP* 3.8 22.7 - + + -
87E MET* 3.2 52.3 - - + -
88E PRO* 4.4 3.4 - - + -
89E SER* 3.3 19.7 + - - +
91E TYR* 1.3 77.3 - - - +
93E MET* 1.3 94.9 + - + +
96E THR* 2.8 30.7 + - - -
117E VAL* 4.0 14.4 - - + -
120E MET* 4.0 11.4 - - + +
121E TRP* 3.6 14.7 + - - +
124E ARG* 4.1 1.4 + - - -
149E THR* 4.0 12.3 - - + -
152E GLU* 2.8 33.6 + - - -
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Residues in contact with MET 93 (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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91E TYR 3.2 0.4 - - - -
92E TYR* 1.3 124.1 - - + +
94E GLU* 1.3 70.7 + - - +
96E THR* 4.0 1.4 - - - -
97E LYS* 3.2 24.8 + - + +
117E VAL* 3.6 19.3 - - + +
118E LYS* 5.5 5.4 - - - -
121E TRP* 3.4 51.6 - - + -
149E THR* 5.7 0.9 - - + -
151E MET* 4.8 4.0 - - + -
186H PHE* 4.3 6.3 - - + -
189H TRP* 3.6 20.3 - - + -
190H GLU* 5.2 8.7 - - - +
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Residues in contact with GLU 94 (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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6E VAL* 3.0 28.8 - - - +
7E GLU* 4.1 11.4 - - + -
10E ALA* 3.4 25.8 - - + -
90E PRO 4.7 0.5 - - - +
91E TYR* 3.1 33.9 - - - +
93E MET* 1.3 79.6 + - - +
95E LEU* 1.3 66.9 + - - +
97E LYS* 3.5 1.4 + - - +
98E LEU* 3.0 30.3 + - + +
149E THR* 5.0 1.4 - - - +
151E MET* 3.4 34.5 + - + +
189H TRP* 3.9 13.9 - - + -
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Residues in contact with LEU 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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10E ALA* 4.2 13.7 - - + +
13E GLU* 4.2 17.7 - - + -
14E LEU 5.7 1.1 - - - +
15E VAL* 5.3 8.7 - - + -
46E LEU* 3.4 30.7 - - + -
63E PRO* 4.6 11.0 - - + -
65E TRP* 3.8 30.7 - - + +
66E MET* 4.3 3.8 - - + -
89E SER* 3.8 13.9 - - - +
91E TYR* 2.9 26.4 + - + +
94E GLU* 1.3 75.0 - - - +
96E THR* 1.3 55.4 - - - +
98E LEU* 3.2 1.6 + - - +
99E LEU* 2.8 43.7 + - + +
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Residues in contact with THR 96 (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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65E TRP* 3.7 12.0 - - - -
66E MET* 3.7 12.2 - - + +
92E TYR 2.8 21.7 + - - -
93E MET 4.0 2.9 - - - -
95E LEU* 1.3 78.0 - - - +
97E LYS* 1.3 63.4 + - - +
99E LEU* 4.1 0.2 - - - -
100E LEU* 3.0 52.4 + - + +
113E ILE* 4.3 9.1 - - + +
114E ARG* 4.9 1.8 - - - -
117E VAL* 3.6 39.9 - - + +
118E LYS* 6.1 2.5 - - - +
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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
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7E GLU* 2.6 30.0 + - - +
93E MET 3.2 17.6 + - - +
94E GLU 3.8 1.8 - - - +
96E THR* 1.3 81.5 - - - +
98E LEU* 1.3 70.5 + - + +
100E LEU* 4.3 1.7 - - - +
101E ASN* 3.0 55.6 + - - +
102E HIS* 5.8 0.8 + - - -
189H TRP* 3.3 42.7 + - + +
190H GLU* 4.3 18.2 - - + +
191H LYS 4.0 4.5 - - - -
192H GLY 5.6 0.8 - - - -
193H GLN* 3.2 23.4 - - - +
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Residues in contact with LEU 98 (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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7E GLU* 3.2 41.1 - - + +
10E ALA* 5.5 0.2 - - + -
11E GLU* 4.2 17.3 - - + +
46E LEU* 3.4 33.9 - - + -
50E ILE* 4.1 13.3 - - + +
94E GLU* 3.0 21.7 + - + +
95E LEU 3.8 2.0 - - - +
97E LYS* 1.3 88.0 - - + +
99E LEU* 1.3 59.5 + - + +
101E ASN* 3.4 1.0 + - + -
102E HIS* 3.1 53.2 + - + +
144G LYS* 6.3 0.7 - - + -
193H GLN* 5.6 0.4 - - - +
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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
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15E VAL* 5.3 7.4 - - + -
46E LEU* 3.7 26.5 - - + -
50E ILE* 4.2 3.6 - - + -
60E LEU* 3.7 31.4 - - + -
61E LEU 5.1 2.9 - - - +
62E PRO* 5.0 2.9 - - + -
63E PRO* 3.6 35.2 - - + -
66E MET* 4.0 12.8 - - + -
95E LEU* 2.8 26.5 + - + +
96E THR 4.3 1.1 - - - +
98E LEU* 1.3 72.8 - - - +
100E LEU* 1.3 55.0 + - - +
103E ALA* 2.7 39.9 + - + +
107E ILE* 3.5 18.1 - - + +
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Residues in contact with LEU 100 (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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66E MET* 4.8 1.1 - - - -
96E THR* 3.0 38.8 + - + +
97E LYS* 4.3 2.7 - - - +
99E LEU* 1.3 76.0 - - - +
101E ASN* 1.3 66.5 + - - +
102E HIS 3.5 0.2 + - - -
104E SER* 3.1 27.5 + - - -
107E ILE* 3.7 28.5 - - + -
110E ALA* 3.9 29.4 - - + +
113E ILE* 4.5 6.7 - - + -
114E ARG* 3.7 50.6 + - + +
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Residues in contact with ASN 101 (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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97E LYS* 3.0 40.9 + - + +
98E LEU* 3.8 4.9 - - - +
100E LEU* 1.3 83.2 - - - +
102E HIS* 1.3 78.4 + - + +
190H GLU 4.7 2.5 + - - +
191H LYS 3.7 21.2 + - - -
192H GLY* 4.9 5.1 - - - -
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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
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50E ILE* 3.5 39.7 - - + +
53E LYS* 3.7 22.8 + - + +
54E GLN* 3.8 25.4 + - + +
97E LYS* 5.8 1.0 + - - -
98E LEU* 3.1 38.9 + - + +
101E ASN* 1.3 95.8 + - + +
103E ALA* 1.3 61.6 + - + +
104E SER* 3.9 0.9 - - - -
105E ASP* 4.3 1.4 - - - +
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Residues in contact with ALA 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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53E LYS* 3.5 16.2 - - - +
60E LEU* 4.0 24.5 - - + -
99E LEU* 2.7 23.7 + - + +
102E HIS* 1.3 78.4 - - - +
104E SER* 1.3 51.8 + - - +
105E ASP* 2.9 14.1 - - - -
106E ASN* 2.7 32.1 + - + +
107E ILE* 3.2 11.6 + - + +
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Residues in contact with SER 104 (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 3.2 4.2 + - - -
100E LEU* 3.1 26.7 + - - +
101E ASN 5.5 0.2 - - - -
102E HIS 3.9 0.6 - - - -
103E ALA* 1.3 77.5 - - - +
105E ASP* 1.3 58.9 + - - +
106E ASN 3.0 1.8 + - - -
107E ILE* 2.9 27.3 + - - +
110E ALA* 4.0 22.4 - - - +
114E ARG* 5.2 4.7 - - - -
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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