Contacts of the helix formed by residues 115 - 124 (chain G) in PDB entry 2E9X
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 HIS 115 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23G ASP* 2.8 43.9 + - - -
26G LEU* 4.4 9.6 - - + -
27G MET* 3.6 37.6 - - + -
30G GLU* 2.7 30.0 + - - +
92G TYR* 4.6 0.2 - - - -
113G GLY* 3.4 2.3 - - - -
114G PRO* 1.3 83.5 - - + +
116G PHE* 1.3 65.0 - - - +
117G TYR 3.4 1.8 - - - -
118G GLY* 4.0 5.4 - - - +
119G PHE* 2.9 23.8 + - - +
169G ASP* 3.6 4.7 - - - -
170G GLU* 3.7 23.1 - - + +
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Residues in contact with PHE 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G ILE* 3.8 23.1 - - + -
92G TYR* 2.7 57.4 + + - -
100G PHE* 3.7 24.0 - + - -
109G LEU* 3.7 26.0 - - + -
112G MET 5.0 2.0 - - - -
113G GLY* 4.0 9.2 - - - -
114G PRO 3.4 1.6 - - - -
115G HIS* 1.3 73.1 - - - +
117G TYR* 1.3 83.2 + + - +
120G GLY* 3.1 11.3 + - - -
137G SER* 5.2 3.4 - - - -
138G LEU* 3.7 23.2 - - + +
141G THR* 3.9 25.8 - - + -
169G ASP* 3.1 17.3 + - + +
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Residues in contact with TYR 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F LEU* 4.1 15.5 - - + -
13G LEU* 3.7 16.6 - - + -
109G LEU* 3.7 2.4 - - + +
115G HIS 3.4 0.4 - - - -
116G PHE* 1.3 99.2 - + - +
118G GLY* 1.3 61.2 + - - +
120G GLY* 3.4 0.9 + - - -
121G SER* 2.8 34.7 + - - -
138G LEU* 3.4 36.1 - - + +
141G THR* 3.5 17.5 - - - +
142G PHE* 3.5 22.9 - - + -
145G ARG* 3.7 0.7 - - - -
169G ASP* 3.3 27.8 + - - +
171G MET* 3.6 22.0 - - + -
172G GLU* 2.9 30.9 + - - -
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Residues in contact with GLY 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ALA* 3.7 24.3 - - - +
13G LEU* 3.9 9.5 - - - +
27G MET* 4.3 5.4 - - - -
115G HIS* 3.4 8.2 + - - +
117G TYR* 1.3 76.3 - - - +
119G PHE* 1.3 65.0 + - - +
121G SER* 3.3 3.5 + - - -
122G GLN* 3.2 27.2 + - - +
169G ASP* 4.9 0.8 + - - -
171G MET* 5.9 1.4 - - - +
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Residues in contact with PHE 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G MET* 3.8 25.5 - - + +
30G GLU* 3.6 47.8 - - + +
31G LYS 3.9 13.0 - - - -
32G LEU* 3.9 34.1 - - + -
70G LEU* 3.9 19.4 - - + +
89G PRO* 3.9 14.1 - - + -
92G TYR* 3.6 20.4 - + - +
115G HIS 2.9 21.4 + - - +
118G GLY* 1.3 71.6 - - - -
120G GLY* 1.3 57.9 + - - +
122G GLN* 3.3 3.8 + - - +
123G LEU* 2.9 33.5 + - + +
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Residues in contact with GLY 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G TYR* 3.3 21.5 + - - -
116G PHE 3.1 19.4 + - - -
117G TYR 3.8 0.7 - - - -
118G GLY 3.2 0.2 - - - -
119G PHE* 1.3 78.6 - - - +
121G SER* 1.3 60.3 + - - +
123G LEU* 3.2 20.5 + - - +
124G LEU* 3.5 12.5 + - - +
134G ILE* 4.4 3.1 - - - +
138G LEU* 3.7 12.7 - - - +
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Residues in contact with SER 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F LEU* 3.8 14.4 - - - +
173F ASN* 4.2 7.8 + - - +
12G ALA 3.3 21.1 - - - -
13G LEU* 3.5 22.9 - - - +
14G GLY 5.0 1.3 - - - +
117G TYR 2.8 20.1 + - - -
118G GLY 3.8 0.4 - - - -
120G GLY* 1.3 76.1 - - - +
122G GLN* 1.3 63.9 + - - +
124G LEU* 3.3 30.1 + - - +
125G HIS* 4.1 6.2 + - - -
138G LEU* 3.7 3.8 - - - +
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Residues in contact with GLN 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ALA* 2.6 30.3 + - + +
14G GLY 3.1 18.2 + - - -
15G PRO 4.1 3.0 + - - -
16G GLU* 3.9 4.0 - - - +
17G GLU* 3.9 10.8 + - - +
27G MET* 3.8 19.5 - - + -
70G LEU* 4.0 19.3 - - + -
74G LYS* 2.7 32.0 + - - +
118G GLY 3.2 16.1 + - - +
119G PHE 3.8 3.8 - - - +
121G SER* 1.3 73.5 - - - +
123G LEU* 1.3 61.3 + - - +
124G LEU 3.0 5.4 - - - -
125G HIS* 3.1 40.4 + - - +
126G PHE* 4.3 6.3 - - - -
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Residues in contact with LEU 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G LEU* 3.5 31.9 - - + -
70G LEU* 5.3 2.0 - - + -
86G VAL* 4.7 3.1 - - + -
88G LEU* 3.8 31.7 - - + +
89G PRO* 4.0 4.3 - - + -
92G TYR* 3.6 38.8 - - + -
119G PHE* 2.9 17.8 + - + +
120G GLY 3.2 13.9 - - - +
121G SER 3.2 0.2 - - - -
122G GLN* 1.3 77.4 - - - +
124G LEU* 1.3 61.1 + - + +
125G HIS 3.0 2.1 + - - -
126G PHE* 3.3 31.7 + - + +
128G SER* 5.4 1.2 + - - -
131G ASN* 4.4 4.0 - - - +
134G ILE* 4.4 8.3 - - + -
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Residues in contact with LEU 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F ASN* 3.5 46.7 - - + +
174F LEU* 4.2 11.7 - - + -
120G GLY 3.6 5.4 - - - +
121G SER* 3.3 21.3 - - - +
122G GLN 3.0 0.4 - - - -
123G LEU* 1.3 78.1 - - - +
125G HIS* 1.3 62.8 + - + +
126G PHE 3.2 0.4 - - - -
127G ASP* 3.3 4.5 + - - +
131G ASN* 3.0 62.3 + - + +
134G ILE* 4.1 21.5 - - + -
135G SER* 4.4 4.0 - - - +
138G LEU* 5.2 1.1 - - + -
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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