Contacts of the strand formed by residues 30 - 35 (chain D) in PDB entry 2LNQ
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 ALA 30 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C MET 3.7 7.2 - - - +
36C VAL* 3.9 15.7 - - + -
27D ASN* 3.6 25.9 + - - +
29D GLY* 1.3 75.8 - - - +
31D ILE* 1.3 63.9 + - - +
32D ILE* 4.6 9.4 - - + +
35E MET* 3.5 1.0 - - - +
36E VAL* 3.0 40.1 + - + +
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Residues in contact with ILE 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 3.7 0.3 - - - -
35C MET* 3.1 62.8 + - + +
38C GLY* 5.5 7.0 - - - -
30D ALA* 1.3 77.3 - - - +
32D ILE* 1.3 80.6 + - - +
34E LEU 3.4 15.3 - - - +
35E MET* 3.7 30.5 - - + -
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Residues in contact with ILE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LEU* 5.0 10.8 - - + -
19C PHE* 4.5 7.0 - - + -
32C ILE* 5.2 0.4 - - + -
33C GLY 3.8 6.5 - - - +
34C LEU* 3.3 30.5 - - + -
35C MET 4.6 1.8 - - - +
36C VAL* 6.1 1.8 - - + -
19D PHE* 3.4 42.4 - - + -
21D ALA* 5.5 4.9 - - + -
30D ALA* 4.6 9.4 - - + +
31D ILE* 1.3 95.3 - - - +
33D GLY* 1.3 65.3 + - - +
34D LEU* 4.8 2.2 - - + -
33E GLY* 3.4 1.0 - - - -
34E LEU* 2.9 48.3 + - + +
36E VAL* 6.3 0.9 - - + -
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Residues in contact with GLY 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ILE* 3.6 1.8 - - - +
33C GLY 3.0 33.9 + - - +
32D ILE* 1.3 75.6 - - - +
34D LEU* 1.3 64.6 + - - +
32E ILE 3.3 11.0 - - - -
33E GLY* 4.0 4.3 - - - -
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Residues in contact with LEU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 4.7 3.4 - - + -
31C ILE 3.8 4.9 - - - -
32C ILE* 3.5 35.7 - - + -
17D LEU* 4.2 19.7 - - + -
19D PHE* 3.3 42.6 - - + -
32D ILE* 4.8 0.7 - - + -
33D GLY* 1.3 80.3 - - - +
35D MET* 1.3 63.1 + - - +
19E PHE* 3.8 13.5 - - + -
31E ILE* 3.5 2.9 - - - +
32E ILE* 2.9 59.9 + - + +
34E LEU* 5.2 1.6 - - + -
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Residues in contact with MET 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLY 4.3 1.0 - - - +
30C ALA* 3.6 1.7 - - - +
31C ILE* 3.0 56.6 + - + +
32C ILE* 5.0 0.5 - - - +
17D LEU* 5.5 0.4 - - - -
34D LEU* 1.3 78.3 - - - +
36D VAL* 1.3 66.3 + - - +
37D GLY 4.5 15.5 - - - +
38D GLY* 5.1 7.9 - - - -
30E ALA 3.4 6.1 - - - +
31E ILE* 3.7 33.0 - - + -
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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