Contacts of the strand formed by residues 7 - 11 (chain L) in PDB entry 2A3W
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 LYS 7 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L ASP 4.9 7.2 + - - +
4L LEU* 3.0 26.3 + - + +
5L SER 4.1 10.1 - - - +
6L GLY* 1.3 85.0 - - - +
8L VAL* 1.3 67.8 + - - +
155L GLY* 4.1 1.6 - - - -
156L ASP* 4.7 1.2 + - - +
185L TRP* 3.2 25.0 + - - -
198L ILE* 3.8 24.9 - - + -
199L LYS 3.3 15.5 - - - +
200L PRO* 4.3 4.9 - - + -
201L LEU* 3.9 3.6 - - - +
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Residues in contact with VAL 8 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L LEU* 6.1 0.7 - - - -
7L LYS* 1.3 79.4 - - - +
9L PHE* 1.3 65.3 + - - +
10L VAL* 4.0 13.2 - - + -
153L GLU* 3.5 22.4 - - + +
154L ILE 3.4 14.4 - - - +
155L GLY* 3.8 11.7 - - - +
185L TRP* 4.1 2.9 - - - -
198L ILE* 3.3 10.0 - - - +
199L LYS* 2.8 40.0 + - + +
200L PRO 3.9 10.3 - - - +
201L LEU* 3.7 30.3 - - + -
203L TRP* 4.0 8.5 - - + -
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Residues in contact with PHE 9 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L LEU* 3.9 15.7 - - + -
8L VAL* 1.3 72.4 - - - +
10L VAL* 1.3 61.7 + - - +
11L PHE* 3.7 19.8 - + + -
20L VAL* 3.9 22.7 - - + -
22L LEU* 4.4 0.2 - - + -
133L LEU* 3.8 22.7 - - + -
152L GLY 3.7 1.0 - - - +
153L GLU* 3.2 6.2 - - - +
154L ILE* 2.8 34.3 + - + +
185L TRP* 3.7 29.1 - + - -
188L LEU* 4.0 6.7 - - + -
190L TYR* 3.8 39.0 - + - -
192L ILE* 4.4 4.3 - - + -
196L VAL* 4.1 12.8 - - + -
197L ILE 3.8 1.1 - - - -
198L ILE* 3.9 25.6 - - + -
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Residues in contact with VAL 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L VAL* 4.0 12.3 - - + -
9L PHE* 1.3 76.0 - - - +
11L PHE* 1.3 62.6 + - - +
12L PRO* 3.1 15.2 - - + +
152L GLY 3.6 5.8 - - - +
153L GLU* 4.2 5.8 - - + -
196L VAL* 3.4 3.4 - - - -
197L ILE 2.7 43.4 + - - +
199L LYS* 3.9 27.8 - - + -
104M ILE* 3.8 25.4 - - + -
116M LYS* 3.9 32.8 - - + +
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Residues in contact with PHE 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L PHE* 3.7 22.0 - - + -
10L VAL* 1.3 72.3 - - - +
12L PRO* 1.3 66.4 - - - +
13L ARG 3.3 7.2 + - - +
18L ASP* 4.4 10.8 - - + -
19L HIS* 4.1 1.1 - - - -
20L VAL* 4.0 14.4 - - + -
133L LEU* 3.6 40.6 - - + -
134L GLY* 3.6 10.5 - - - -
150L PHE* 3.3 37.9 - + - +
151L VAL* 3.4 4.1 - - - +
152L GLY* 2.8 41.7 + - - +
154L ILE* 4.2 13.5 - - + -
195L TYR 4.4 1.3 - - - +
196L VAL* 3.8 28.3 - - + -
116M LYS 4.9 0.3 - - - +
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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