Contacts of the helix formed by residues 131 - 145 (chain L) in PDB entry 2GTL
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 ASP 131 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60H ASN* 4.9 1.6 + - - -
62H TYR* 5.5 0.2 - - - -
126K GLN* 4.4 3.6 - - - +
13L GLU* 5.7 0.5 - - - +
16L LYS* 2.9 46.7 + - + +
20L GLN* 3.2 11.7 + - - +
129L HIS 3.0 5.0 + - - +
130L PHE* 1.3 67.4 - - - +
132L PHE* 1.3 62.5 + - - +
133L GLY* 3.5 5.7 + - - -
134L ALA* 3.1 29.0 + - + +
135L TRP* 3.0 24.6 + - - -
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Residues in contact with PHE 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H ASP 3.9 20.2 - - - -
60H ASN* 3.4 28.0 - - + +
61H ILE* 5.5 3.8 - - + -
62H TYR* 3.8 37.1 - + + +
119L LEU* 4.2 24.9 - - + -
130L PHE* 3.0 29.3 + + + -
131L ASP* 1.3 68.7 + - - +
133L GLY* 1.3 69.1 + - - +
135L TRP* 3.0 2.9 + - - +
136L HIS* 2.8 49.9 + + + -
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Residues in contact with GLY 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H ARG* 5.7 2.7 - - - -
60H ASN* 2.8 25.9 - - - +
13L GLU* 5.4 1.6 - - - -
131L ASP* 3.2 5.5 + - - -
132L PHE* 1.3 77.5 - - - +
134L ALA* 1.3 62.8 + - - +
136L HIS* 3.7 2.8 - - - +
137L ASP* 3.0 31.5 + - - +
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Residues in contact with ALA 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L CYS* 4.7 0.5 - - - -
13L GLU* 3.6 38.9 + - + +
16L LYS* 4.3 4.7 - - + -
17L VAL* 3.8 7.8 - - + +
131L ASP* 3.1 36.0 + - + +
133L GLY* 1.3 72.8 - - - +
135L TRP* 1.3 58.6 + - - +
137L ASP* 3.7 4.2 + - - +
138L CYS* 2.9 31.9 + - - +
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Residues in contact with TRP 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L VAL* 3.4 39.6 - - + +
20L GLN* 2.8 29.2 - - + +
21L TRP* 3.6 46.4 - + + -
81L ILE* 4.0 10.1 - - + -
118L LEU* 4.9 4.3 - - + -
119L LEU* 3.6 17.5 - - + -
122L LEU* 3.2 34.3 - - + -
126L LEU* 4.8 1.3 - - + -
130L PHE* 3.2 19.7 - + + -
131L ASP* 3.0 21.6 + - + +
132L PHE 3.0 6.0 + - - +
134L ALA* 1.3 73.1 - - + +
136L HIS* 1.3 63.1 + - - +
138L CYS* 2.8 1.5 + - - -
139L VAL* 2.6 66.9 + - + +
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Residues in contact with HIS 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115L LEU* 4.2 13.7 - - + +
119L LEU* 3.7 23.0 - - + +
132L PHE* 2.8 42.7 + + + +
133L GLY* 3.7 3.6 - - - +
135L TRP* 1.3 73.7 - - - +
137L ASP* 1.3 71.3 + - - +
139L VAL* 5.4 1.1 - - - -
140L ASP* 2.9 45.2 + - - +
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Residues in contact with ASP 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L GLU 3.6 36.8 + - - +
9L CYS* 4.2 7.2 + - - +
13L GLU* 3.4 20.9 - - - +
133L GLY* 3.0 18.2 + - - +
134L ALA* 3.9 3.6 - - - +
136L HIS* 1.3 88.0 - - - +
138L CYS* 1.3 60.6 + - - +
140L ASP* 4.0 2.9 - - - +
141L GLN* 3.8 15.6 + - - +
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Residues in contact with CYS 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L CYS* 2.0 44.6 - - - -
13L GLU 4.3 2.9 - - - -
14L SER* 4.4 0.2 - - - -
17L VAL* 4.0 12.6 - - + -
84L LEU* 3.3 37.4 - - + +
134L ALA 2.9 19.3 + - - +
135L TRP 2.8 3.8 + - - +
137L ASP* 1.3 75.8 - - - +
139L VAL* 1.3 64.2 + - - +
140L ASP 3.1 1.6 - - - -
141L GLN* 3.4 17.4 + - - +
142L ILE* 3.6 11.8 + - - +
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Residues in contact with VAL 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L VAL* 5.0 4.0 - - + -
77L LEU* 5.0 7.4 - - + -
81L ILE* 5.1 4.3 - - + -
114L PHE* 5.7 1.6 - - + -
115L LEU* 3.4 27.8 - - + -
118L LEU* 4.2 17.9 - - + -
119L LEU* 5.1 0.7 - - + -
135L TRP* 2.6 57.0 + - + +
138L CYS* 1.3 70.1 - - - +
140L ASP* 1.3 66.1 + - - +
142L ILE* 2.9 27.4 + - + +
143L ILE* 3.0 18.1 + - + +
160L HEM 5.8 0.4 - - + -
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Residues in contact with ASP 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L ASP* 5.6 1.4 - - - +
115L LEU* 4.0 23.7 - - + +
136L HIS* 2.9 37.9 + - - +
137L ASP* 4.0 4.9 - - - +
138L CYS 3.1 0.2 - - - -
139L VAL* 1.3 77.5 - - - +
141L GLN* 1.3 55.5 + - - +
143L ILE* 2.7 30.3 + - - +
144L ASP* 3.0 37.4 + - - +
147L LYS* 5.3 1.7 + - - -
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Residues in contact with GLN 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L GLU* 5.8 0.8 - - - +
9L CYS* 3.7 33.9 + - - +
84L LEU* 5.8 2.2 - - - +
90L LEU* 3.8 25.8 - - + +
94L LEU* 4.0 9.4 - - + +
137L ASP 3.8 7.2 + - - +
138L CYS* 3.4 11.8 + - - +
139L VAL 3.3 0.4 - - - -
140L ASP* 1.3 77.3 - - - +
142L ILE* 1.3 60.6 + - + +
144L ASP* 3.9 11.0 + - - +
145L GLY 3.5 13.7 + - - -
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Residues in contact with ILE 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L LEU* 4.8 10.3 - - + -
80L THR* 3.4 35.0 - - + +
81L ILE* 4.0 13.7 - - + +
84L LEU* 3.5 31.6 - - + -
90L LEU* 4.7 6.5 - - + -
94L LEU* 3.3 32.7 - - + +
138L CYS 3.6 13.7 - - - +
139L VAL* 2.9 19.1 + - + +
140L ASP 2.9 0.2 + - - -
141L GLN* 1.3 77.1 - - + +
143L ILE* 1.3 63.8 + - + +
145L GLY 3.6 1.6 + - - -
146L ILE* 3.4 15.8 - - + +
160L HEM 5.3 4.7 - - + -
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Residues in contact with ILE 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111L PHE* 3.3 41.3 - - + +
112L ASP* 4.8 2.7 - - - +
114L PHE* 4.7 4.9 - - + -
115L LEU* 3.2 49.8 - - + +
139L VAL* 3.0 16.8 + - + +
140L ASP* 2.7 15.8 + - - +
142L ILE* 1.3 67.9 - - + +
144L ASP* 1.3 53.1 + - - +
145L GLY 3.0 1.6 - - - -
146L ILE* 2.6 31.7 + - - +
147L LYS* 2.7 31.3 + - - -
160L HEM 4.2 17.5 - - + -
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Residues in contact with ASP 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98L LYS* 5.0 5.5 + - - -
140L ASP* 3.0 31.8 + - - +
141L GLN* 4.2 7.9 - - - +
143L ILE* 1.3 76.7 - - - +
145L GLY* 1.3 58.3 + - - +
146L ILE 3.1 4.7 + - - -
147L LYS* 3.2 43.2 + - - +
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Residues in contact with GLY 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L LEU* 3.5 33.8 - - - +
95L ALA* 4.4 1.4 + - - -
98L LYS* 3.5 16.3 - - - +
141L GLN 3.5 11.3 + - - -
142L ILE 3.6 4.2 + - - -
143L ILE 2.9 1.8 + - - -
144L ASP* 1.3 78.4 - - - +
146L ILE* 1.3 60.6 + - - +
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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