Contacts of the helix formed by residues 9 - 20 (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 ASN 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLU* 3.2 30.9 + - + +
8A ILE* 1.3 88.4 + - - +
10A PRO* 1.3 77.7 - - + +
11A GLU* 3.3 10.3 + - + +
12A MET* 3.4 17.0 + - + +
13A LEU* 3.4 27.1 + - - +
151A GLN* 5.9 2.0 + - - -
215A SER* 5.8 1.2 + - - -
217A VAL* 5.2 1.1 - - - -
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Residues in contact with PRO 10 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ASN* 1.3 90.1 - - + +
11A GLU* 1.3 60.9 + - + +
13A LEU* 3.6 2.3 + - + +
14A ASN* 3.0 39.9 + - - +
28A PHE* 3.3 42.8 - - + +
29A VAL* 5.8 1.1 - - - -
217A VAL* 4.4 13.5 - - + -
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Residues in contact with GLU 11 (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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9A ASN* 5.0 8.7 - - + +
10A PRO* 1.3 81.4 - - + +
12A MET* 1.3 65.1 + - + +
14A ASN* 3.7 4.8 - - - +
15A LYS* 2.9 51.0 + - + +
149A GLU 5.6 1.2 - - - +
150A GLY* 5.9 2.3 - - - -
151A GLN* 5.1 7.1 + - - +
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Residues in contact with MET 12 (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* 3.7 38.8 - - + +
7A GLU* 3.9 22.0 - - - +
9A ASN* 3.4 16.6 + - + +
11A GLU* 1.3 83.8 - - + +
13A LEU* 1.3 57.1 + - + +
15A LYS* 3.4 9.9 + - - +
16A VAL* 3.1 32.7 + - - +
146A VAL* 3.5 32.9 - - + +
147A ALA* 3.8 11.9 - - - +
150A GLY* 4.1 17.7 - - - -
151A GLN* 5.1 7.4 - - - +
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Residues in contact with LEU 13 (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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8A ILE* 4.2 19.7 - - + -
9A ASN 3.4 24.1 + - - +
10A PRO 3.8 1.8 - - - +
11A GLU 3.3 0.4 - - - -
12A MET* 1.3 73.9 - - + +
14A ASN* 1.3 64.9 + - - +
16A VAL* 3.3 8.0 + - + +
17A LEU* 3.2 26.5 + - - +
28A PHE* 3.5 50.0 - - + -
50A LEU* 6.1 1.1 - - + -
91A GLY* 3.8 35.4 - - - +
94A GLY* 5.7 0.4 - - - -
95A LEU* 3.9 19.8 - - + +
217A VAL* 4.6 1.8 - - + -
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Residues in contact with ASN 14 (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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10A PRO* 3.0 24.6 + - - +
11A GLU* 3.7 5.1 - - - +
13A LEU* 1.3 70.6 - - - +
15A LYS* 1.3 64.8 + - - +
17A LEU* 3.3 12.4 + - - +
18A TYR* 3.1 48.3 + - + -
27A ARG* 4.0 18.2 - - - +
28A PHE* 3.7 28.5 + - - +
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Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLU* 2.9 37.5 + - + +
12A MET* 3.5 11.7 - - - +
14A ASN* 1.3 75.4 - - - +
16A VAL* 1.3 57.1 + - - +
18A TYR* 3.8 4.3 - - + +
19A ARG* 2.9 33.8 + - - +
146A VAL* 4.1 18.6 - - + -
149A GLU* 5.3 12.4 + - - +
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Residues in contact with VAL 16 (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* 6.4 0.4 - - + -
12A MET* 3.1 16.0 + - + +
13A LEU* 3.3 8.7 + - - +
15A LYS* 1.3 74.2 - - - +
17A LEU* 1.3 64.7 + - - +
19A ARG* 3.5 50.9 - - - +
20A LEU* 3.6 12.3 + - - +
95A LEU* 3.6 35.4 - - + -
114A LEU* 5.0 9.9 - - + -
143A HIS* 4.2 9.6 - - + +
146A VAL* 3.8 17.2 - - + +
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Residues in contact with LEU 17 (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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13A LEU 3.2 15.3 + - - +
14A ASN* 3.3 19.0 + - - +
16A VAL* 1.3 78.8 - - - +
18A TYR* 1.3 71.0 + - + +
20A LEU* 3.3 9.1 + - - +
22A VAL* 3.4 47.9 + - + +
23A ALA 5.5 4.3 - - - +
24A GLY* 6.2 0.7 - - - -
26A TRP* 3.6 28.7 - - + +
28A PHE* 4.5 15.0 - - + -
95A LEU* 4.2 15.3 - - + -
99A VAL* 5.2 9.4 - - + -
106A LEU* 4.9 8.7 - - + -
114A LEU* 5.9 3.1 - - + -
219A LEU* 5.6 0.2 - - + -
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Residues in contact with TYR 18 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASN* 3.1 43.2 + - + +
15A LYS* 4.2 4.3 - - + +
17A LEU* 1.3 77.0 - - + +
19A ARG* 1.3 63.1 + - - +
21A GLY* 3.0 14.9 + - - +
22A VAL 3.8 13.5 - - - +
24A GLY* 3.6 37.3 + - - -
26A TRP 5.6 0.7 + - - -
27A ARG* 6.0 2.4 - - - +
224A LEU* 4.6 7.0 - - + +
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Residues in contact with ARG 19 (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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15A LYS 2.9 19.3 + - - +
16A VAL* 3.5 39.9 + - - +
18A TYR* 1.3 73.9 - - - +
20A LEU* 1.3 84.1 + - + +
21A GLY 3.3 0.8 + - - -
113A VAL* 5.2 4.4 - - - +
114A LEU* 5.6 1.6 - - - +
139A ILE* 5.2 1.8 - - - +
142A ALA* 2.9 54.5 + - + +
143A HIS* 3.4 25.9 + - - +
145A ALA* 5.7 2.0 - - - -
146A VAL* 4.3 13.3 - - + +
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Residues in contact with LEU 20 (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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16A VAL* 3.7 11.4 - - + +
17A LEU* 3.3 10.3 + - - +
19A ARG* 1.3 102.2 - - + +
21A GLY* 1.3 60.2 + - - +
22A VAL* 3.4 15.3 + - + +
108A PHE* 6.0 0.2 - - - +
111A GLY* 4.2 14.1 - - - +
112A SER* 4.1 20.0 + - - -
113A VAL* 3.8 28.3 - - + +
114A LEU* 3.8 36.3 - - + +
142A ALA* 5.6 3.1 - - + -
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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