Contacts of the helix formed by residues 137 - 150 (chain A) in PDB entry 2LEN
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 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 6.1 5.4 - - + -
135A LYS 4.1 7.6 - - - +
136A ASN* 1.3 81.3 - - - +
138A ALA* 1.3 60.9 + - - +
139A ILE 3.6 0.2 - - - -
140A GLN* 3.5 0.6 + - - -
141A ALA* 2.9 36.0 + - - +
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A VAL* 4.5 19.3 - - + -
136A ASN* 4.7 3.1 - - - +
137A GLU* 1.3 77.8 - - - +
139A ILE* 1.3 63.1 + - + +
141A ALA* 4.1 2.0 - - - +
142A ALA* 3.0 27.3 + - - +
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Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG* 5.2 1.8 - - - +
113A VAL* 3.7 34.1 - - + +
114A LEU* 5.1 10.5 - - + -
117A PHE* 3.7 48.2 - - + -
133A PHE* 3.7 28.7 - - + -
136A ASN* 3.8 21.4 - - - +
137A GLU 3.6 0.2 - - - -
138A ALA* 1.3 73.7 - - - +
140A GLN* 1.3 57.3 + - - +
142A ALA* 3.3 4.7 + - - +
143A HIS* 2.9 55.0 + - + +
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Residues in contact with GLN 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.2 44.5 + - - +
2A GLN* 4.9 1.5 - - - +
3A LEU* 3.3 34.5 - - + +
86A ILE* 4.3 6.1 - - + +
133A PHE* 2.9 29.6 + - + +
134A GLU* 3.0 23.2 + - - +
136A ASN* 3.3 28.7 + - + +
137A GLU* 3.5 2.6 + - - +
138A ALA 3.3 0.6 - - - -
139A ILE* 1.3 80.0 - - - +
141A ALA* 1.3 62.2 + - - +
143A HIS* 3.5 0.6 + - - -
144A ASP* 3.1 20.0 + - - +
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLU 2.9 21.4 + - - +
138A ALA* 4.1 2.0 - - - +
140A GLN* 1.3 73.1 - - - +
142A ALA* 1.3 56.4 + - - +
144A ASP* 3.3 8.1 + - - +
145A ALA* 2.9 29.3 + - - +
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG* 2.9 47.2 + - + +
20A LEU* 5.6 2.9 - - + -
138A ALA 3.0 20.4 + - - +
139A ILE* 3.3 3.8 + - - +
141A ALA* 1.3 76.8 - - - +
143A HIS* 1.3 57.9 + - - +
145A ALA* 3.6 8.8 - - - +
146A VAL* 3.5 15.9 + - - +
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Residues in contact with HIS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 3.5 25.7 - - + +
6A MET* 4.2 9.8 - - + +
16A VAL* 4.2 9.4 - - + +
19A ARG* 3.4 27.4 + - - +
89A SER* 3.9 16.5 + - - +
90A CYS 5.7 0.8 + - - -
92A THR* 3.9 20.5 - - + +
95A LEU* 4.2 21.5 - - + +
114A LEU* 5.4 6.1 - - - +
133A PHE* 5.1 2.5 - + - -
139A ILE* 2.9 42.5 + - + +
142A ALA* 1.3 73.4 - - - +
144A ASP* 1.3 64.8 + - - +
146A VAL* 3.2 8.9 - - + +
147A ALA* 3.1 22.6 + - - +
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Residues in contact with ASP 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A GLN 4.0 15.6 - - - +
3A LEU* 4.2 4.4 - - + +
4A LYS* 3.5 34.4 + - - +
140A GLN 3.1 14.2 + - - +
141A ALA* 3.6 10.1 - - - +
143A HIS* 1.3 75.0 - - - +
145A ALA* 1.3 57.0 + - - +
147A ALA* 3.2 5.5 + - - +
148A GLN* 2.9 51.7 + - - +
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Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG* 5.7 1.6 - - - -
141A ALA 2.9 17.1 + - - +
142A ALA* 3.6 11.2 - - - +
143A HIS 3.3 0.2 - - - -
144A ASP* 1.3 75.5 - - - +
146A VAL* 1.3 63.2 + - + +
148A GLN* 3.4 8.0 + - - +
149A GLU* 3.3 27.1 + - - +
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A MET* 4.8 9.9 - - + -
12A MET* 3.5 19.2 - - + +
15A LYS* 4.1 27.6 - - + -
16A VAL* 3.8 24.0 - - + +
19A ARG* 4.3 17.5 - - + -
142A ALA 3.5 12.0 + - - +
143A HIS* 3.2 17.9 - - + +
145A ALA* 1.3 76.0 - - + +
147A ALA* 1.3 56.7 + - - +
149A GLU* 3.4 15.7 + - - +
150A GLY* 3.1 21.5 + - - -
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 6.1 0.2 - - + -
4A LYS* 3.9 37.2 - - + +
5A PRO 5.0 4.1 - - - +
6A MET* 4.2 10.1 - - + -
12A MET* 3.8 11.7 - - + -
143A HIS 3.1 17.7 + - - +
144A ASP* 3.2 8.0 + - - +
146A VAL* 1.3 77.0 - - - +
148A GLN* 1.3 57.0 + - - +
150A GLY* 3.1 23.9 + - - +
151A GLN 4.1 5.4 + - - +
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Residues in contact with GLN 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LYS* 4.4 24.7 - - + +
144A ASP* 2.9 37.8 + - - +
145A ALA* 3.4 8.3 + - - +
147A ALA* 1.3 74.6 - - - +
149A GLU* 1.3 61.6 + - + +
150A GLY 3.6 6.1 + - - +
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Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLU* 5.6 1.2 - - - +
15A LYS* 5.3 12.7 + - - +
145A ALA* 3.3 14.6 + - - +
146A VAL* 3.8 16.6 - - - +
147A ALA 3.4 0.2 - - - -
148A GLN* 1.3 76.5 - - + +
150A GLY* 1.3 60.4 + - - +
151A GLN* 4.3 3.8 - - - +
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Residues in contact with GLY 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLU* 5.9 2.5 - - - -
12A MET* 4.1 17.3 - - - -
146A VAL 3.1 13.3 + - - -
147A ALA 3.1 15.1 + - - +
148A GLN 3.7 6.1 - - - +
149A GLU* 1.3 78.3 - - - +
151A GLN* 1.3 72.4 + - - +
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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