Contacts of the strand formed by residues 41 - 46 (chain A) in PDB entry 2NA1
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 PHE 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A VAL* 5.1 1.3 - - - -
38A ILE* 2.2 35.2 + - - +
39A GLU 3.3 0.6 + - - -
40A GLY* 1.3 85.5 - - - +
42A VAL* 1.3 82.5 + - + +
130A ILE* 5.6 5.8 - - + -
167A PRO* 3.2 39.3 - - + -
170A MET* 3.4 14.7 - - + +
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Residues in contact with VAL 42 (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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35A THR* 3.3 29.2 - - + -
36A HIS 3.2 20.2 - - - +
37A VAL* 3.7 27.1 - - + +
41A PHE* 1.3 95.6 - - + +
43A ILE* 1.3 60.0 + - - +
44A GLN* 4.3 3.0 + - + +
167A PRO* 5.1 0.2 - - - +
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Residues in contact with ILE 43 (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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34A LEU 4.0 0.3 - - - +
36A HIS* 2.9 35.4 + - - +
38A ILE* 3.4 36.3 - - + -
42A VAL* 1.3 77.5 - - - +
44A GLN* 1.3 61.0 + - - +
45A GLU 4.2 0.5 + - - -
164A LEU* 3.5 34.8 - - + -
165A ARG 4.5 2.5 - - - +
166A CYS* 3.8 10.8 - - - -
167A PRO* 3.7 28.0 - - + -
170A MET* 4.2 4.3 - - + -
175A LEU* 4.6 2.0 - - + -
178A PHE* 3.7 30.3 - - + -
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Residues in contact with GLN 44 (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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33A ILE* 3.5 23.6 - - + +
34A LEU 3.0 7.9 - - - +
35A THR* 2.7 35.9 + - + +
42A VAL* 5.2 3.1 - - + +
43A ILE* 1.3 75.6 - - - +
45A GLU* 1.3 60.3 + - - +
163A TYR 4.5 0.3 - - - +
164A LEU* 2.9 15.3 - - - +
165A ARG* 4.0 10.7 + - - +
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Residues in contact with GLU 45 (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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32A GLN 4.0 0.2 - - - +
33A ILE* 4.0 3.6 - - - +
34A LEU* 2.8 38.0 + - - +
43A ILE 4.2 0.2 + - - -
44A GLN* 1.3 75.2 - - - +
46A GLY* 1.3 62.2 + - - +
135A ILE* 3.5 22.8 - - - +
162A ARG* 2.9 34.4 + - + +
163A TYR 3.3 16.2 - - - +
164A LEU* 3.4 25.5 - - + +
175A LEU* 5.6 0.3 - - - +
178A PHE* 3.0 46.3 - - + -
182A LYS* 6.2 0.4 - - + -
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Residues in contact with GLY 46 (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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32A GLN 3.2 10.5 - - - -
33A ILE* 3.6 5.6 - - - +
45A GLU* 1.3 79.3 - - - +
47A ALA* 1.3 60.8 + - - -
48A GLU 2.9 9.7 + - - -
162A ARG* 4.0 14.9 - - - -
163A TYR* 2.9 32.4 + - - +
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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