Contacts of the strand formed by residues 18 - 24 (chain A) in PDB entry 3NAV
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 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.6 2.2 - - + -
8A PHE* 4.1 19.1 - - + -
11A LEU* 3.9 16.1 - - + +
17A GLY* 1.3 74.5 - - - -
19A PHE* 1.3 58.5 + - - +
20A VAL* 4.2 8.5 - - + -
46A ASP* 3.3 14.1 - - + +
209A LEU* 4.3 5.6 - - + -
220A VAL* 4.9 0.3 - - - +
224A ILE* 4.9 0.2 - - - +
229A ALA 2.9 15.4 + - - +
230A GLY* 3.1 5.2 - - - -
231A ALA 3.0 25.6 + - - -
266A THR* 3.9 6.7 - - - +
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Residues in contact with PHE 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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18A ALA* 1.3 72.4 - - - +
20A VAL* 1.3 69.0 + - - +
21A PRO* 4.0 30.3 - - + -
45A ALA* 3.8 3.7 - - - -
46A ASP* 2.9 38.4 + - - +
220A VAL* 4.4 11.0 - - + -
231A ALA 3.6 7.4 - - - -
232A ILE 5.1 0.4 - - - -
233A SER* 3.8 25.8 - - - -
237A VAL* 4.7 0.4 - - + -
258A PHE* 4.7 6.7 - + - -
259A THR* 4.1 30.3 - - + -
262A MET* 3.6 42.4 - - + +
263A LYS* 4.2 11.2 - - + -
266A THR* 3.9 15.4 - - + +
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Residues in contact with VAL 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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4A TYR* 6.2 0.4 - - + -
7A LEU* 5.8 0.7 - - + -
18A ALA* 4.5 11.9 - - + -
19A PHE* 1.3 81.5 - - - +
21A PRO* 1.3 62.3 - - - +
47A ALA* 3.7 35.2 - - + +
48A LEU 3.9 2.0 - - - +
49A GLU* 3.8 32.5 - - + +
173A TYR* 5.7 2.5 - - + +
209A LEU* 4.2 21.8 - - + -
231A ALA 2.9 11.6 + - - +
232A ILE* 3.1 21.1 - - + +
233A SER 3.0 23.2 + - - -
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Residues in contact with PRO 21 (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 PHE* 3.9 18.4 - - + +
20A VAL* 1.3 86.3 - - - +
22A PHE* 1.3 60.6 + - - +
23A VAL* 4.3 0.3 + - - +
40A LEU* 3.9 30.8 - - + +
45A ALA* 3.4 24.9 - - + -
47A ALA 3.3 15.9 - - - +
48A LEU* 4.0 6.5 - - + +
49A GLU* 3.1 24.3 + - - +
50A LEU* 5.7 0.2 - - - +
233A SER 3.9 4.7 - - - +
237A VAL* 3.6 20.6 - - + -
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Residues in contact with PHE 22 (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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21A PRO* 1.3 73.4 - - - +
23A VAL* 1.3 85.9 + - - +
24A THR* 4.0 12.1 - - - -
49A GLU* 3.1 36.3 - - + +
50A LEU 3.8 1.8 - - - -
51A GLY* 3.5 30.5 - - - -
64A ILE* 3.7 32.8 - - + -
100A LEU* 4.1 16.6 - - + -
232A ILE* 4.6 6.1 - - + -
233A SER 3.0 18.7 + - - +
234A GLY* 3.7 12.8 - - - +
237A VAL* 3.6 13.5 - - - +
238A VAL* 3.7 9.7 - - + +
601A EDO 3.9 19.1 - - - +
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Residues in contact with VAL 23 (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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21A PRO 4.3 0.4 + - - +
22A PHE* 1.3 86.0 - - - +
24A THR* 1.3 66.8 + - - +
25A ILE* 3.8 0.6 + - - +
27A ASP 6.1 0.2 - - - +
33A SER* 5.6 1.6 - - - +
36A ILE* 4.1 15.5 - - + -
37A MET* 4.1 17.0 - - + -
40A LEU* 3.7 26.7 - - + -
49A GLU 3.2 3.2 + - - -
50A LEU* 3.3 27.6 - - + -
51A GLY 3.0 21.1 + - - -
237A VAL* 3.7 14.1 - - + -
238A VAL* 4.1 4.9 - - + -
241A ILE* 4.2 13.5 - - + -
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Residues in contact with THR 24 (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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22A PHE* 4.0 7.9 - - - -
23A VAL* 1.3 79.0 - - - +
25A ILE* 1.3 75.2 + - - +
26A GLY 3.5 0.2 + - - -
27A ASP* 3.4 20.0 + - + +
33A SER* 4.1 3.3 + - - -
51A GLY 3.6 12.6 + - - +
53A PRO* 4.1 12.8 - - + -
64A ILE* 3.9 12.6 - - - +
67A ALA* 3.5 27.7 - - - +
68A ASN* 3.3 26.8 + - - +
71A ALA* 4.3 8.7 - - + -
238A VAL* 4.5 3.6 - - - +
241A ILE* 6.0 0.2 - - - +
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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