Contacts of the strand formed by residues 12 - 18 (chain A) in PDB entry 2N5T
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 12 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 1.3 89.5 - - - +
13A PHE* 1.3 70.9 + - - +
157A ILE* 5.3 6.1 - - + -
177A LEU* 4.0 31.6 - - + +
178A GLY* 5.8 0.4 - - - -
200A PRO* 4.3 8.7 - - + -
218A LEU 4.9 0.2 - - - -
219A ILE* 3.5 1.4 - - - -
220A LEU* 2.9 40.5 + - + +
243A GLN* 4.4 0.9 - - - -
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Residues in contact with PHE 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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11A ILE* 3.0 34.1 - - + -
12A ALA* 1.3 76.3 - - - +
14A GLY* 1.3 58.2 + - - +
157A ILE* 4.5 2.2 - - - -
177A LEU* 5.0 11.0 - - - +
217A TYR* 3.3 16.4 - - - +
218A LEU 4.0 5.6 - - - -
219A ILE* 3.2 35.0 - - + -
236A ILE* 3.7 26.5 - - + -
239A MET* 3.6 8.1 - - + -
240A ARG* 3.5 36.3 - - + -
243A GLN* 3.2 21.5 - - - -
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Residues in contact with GLY 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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13A PHE* 1.3 75.7 - - - +
15A LYS* 1.3 65.9 - - - +
155A GLU 5.6 1.6 - - - -
156A VAL* 5.5 1.8 - - - -
157A ILE* 3.5 14.0 - - - +
177A LEU* 5.8 1.6 - - - -
217A TYR* 3.8 14.6 - - - -
218A LEU 3.1 32.5 + - - +
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Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLY* 1.3 77.1 - - - -
16A ALA* 1.3 57.7 + - - +
154A ASP* 5.6 8.3 + - + +
155A GLU 4.6 7.7 + - - +
156A VAL* 4.3 22.3 - - + +
157A ILE* 2.6 36.2 + - - +
215A ASP* 3.6 31.8 + - - +
216A ASP 3.3 8.5 - - - +
217A TYR* 4.4 12.8 - - + +
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Residues in contact with ALA 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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15A LYS* 1.3 74.4 - - - +
17A LEU* 1.3 60.8 + - - +
156A VAL* 5.2 1.1 - - - -
157A ILE* 3.9 6.1 - - + -
159A VAL* 4.4 7.6 - - + -
212A VAL* 3.4 32.1 - - + -
214A ASN* 3.3 4.5 - - - -
215A ASP* 2.9 28.4 + - - -
216A ASP* 2.6 20.2 + - + +
218A LEU* 3.4 17.7 - - + -
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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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16A ALA* 1.3 73.4 - - - +
18A LEU* 1.3 69.1 + - - +
19A LEU* 4.3 7.2 - - + -
147A ILE* 3.8 25.4 - - + -
149A LEU* 3.7 29.8 - - + -
152A ILE* 3.9 14.8 - - + -
156A VAL* 4.2 20.4 - - + -
157A ILE 2.9 19.8 + - - +
158A LEU* 4.1 10.1 - - + -
159A VAL* 3.0 31.8 + - - +
212A VAL* 6.2 0.4 - - - -
214A ASN* 4.8 8.3 - - + +
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Residues in contact with LEU 18 (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 ALA 4.0 1.2 + - - -
17A LEU* 1.3 80.6 - - - +
19A LEU* 1.3 69.5 + - - +
20A LYS* 3.2 41.1 + - + +
145A LYS* 5.2 2.6 - - - +
147A ILE* 4.4 10.0 - - - +
159A VAL* 4.2 10.1 - - + +
160A ALA* 5.3 1.3 - - - -
209A THR* 3.7 38.8 - - - +
212A VAL* 3.6 22.0 - - + +
213A LYS* 4.5 7.6 - - + -
214A ASN* 4.1 23.5 - - + +
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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