Contacts of the helix formed by residues 2374 - 2383 (chain F) in PDB entry 1PDW
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 GLY2374 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2369F VAL 4.3 0.2 - - - +
2370F GLU* 2.8 28.4 + - - -
2372F LEU 3.8 0.8 - - - -
2373F ASN* 1.3 80.8 - - - +
2375F LYS* 1.3 65.6 + - - -
2376F GLU 3.4 2.5 - - - -
2377F VAL 3.5 0.7 + - - -
2378F ALA 3.3 16.6 + - - -
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Residues in contact with LYS2375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2370F GLU* 2.4 49.3 + - + +
2374F GLY* 1.3 69.0 - - - -
2376F GLU* 1.3 66.2 + - - +
2378F ALA* 3.4 4.5 + - - +
2379F ALA* 3.1 24.6 + - - +
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Residues in contact with GLU2376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2374F GLY 3.4 0.6 - - - -
2375F LYS* 1.3 78.1 - - - +
2377F VAL* 1.3 65.7 + - + +
2379F ALA* 3.4 5.2 + - - +
2380F GLN* 3.0 47.6 + - + +
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Residues in contact with VAL2377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2229F ALA* 4.2 21.1 - - + +
2369F VAL* 4.0 10.5 - - + -
2373F ASN* 3.3 45.3 - - + +
2374F GLY 3.5 1.4 + - - +
2375F LYS 3.3 0.2 - - - -
2376F GLU* 1.3 80.7 - - + +
2378F ALA* 1.3 62.4 + - - +
2380F GLN* 3.4 16.4 + - - +
2381F VAL* 3.2 25.2 + - + +
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Residues in contact with ALA2378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2366F LEU* 3.7 23.6 - - + +
2369F VAL* 3.7 21.3 - - + -
2370F GLU* 4.0 12.8 - - + +
2374F GLY 3.3 14.6 + - - +
2375F LYS* 3.7 5.6 - - - +
2376F GLU 3.3 0.2 - - - -
2377F VAL* 1.3 79.4 - - - +
2379F ALA* 1.3 58.6 + - - +
2381F VAL* 3.4 4.2 + - - +
2382F LYS* 2.9 29.4 + - - +
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Residues in contact with ALA2379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2375F LYS 3.1 17.1 + - - +
2376F GLU* 3.8 6.7 - - - +
2377F VAL 3.3 0.2 - - - -
2378F ALA* 1.3 74.8 - - - +
2380F GLN* 1.3 60.1 + - + +
2382F LYS* 3.7 9.6 - - + +
2383F ALA* 3.0 30.5 + - - +
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Residues in contact with GLN2380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2376F GLU* 3.0 38.0 + - + +
2377F VAL* 3.9 19.1 - - - +
2378F ALA 3.4 0.2 - - - -
2379F ALA* 1.3 76.6 - - + +
2381F VAL* 1.3 59.8 + - + +
2383F ALA* 3.9 4.6 - - - +
2384F PRO* 3.0 27.0 - - - +
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Residues in contact with VAL2381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2225F VAL* 3.9 34.1 - - + +
2228F ARG* 3.8 24.8 + - + +
2229F ALA* 3.6 32.8 - - + -
2366F LEU* 4.4 4.7 - - + -
2369F VAL* 4.8 1.6 - - + -
2377F VAL* 3.2 20.3 + - + +
2378F ALA* 3.6 6.7 - - - +
2380F GLN* 1.3 79.0 - - + +
2382F LYS* 1.3 59.9 + - - +
2384F PRO* 3.4 10.7 - - - +
2385F LEU* 3.4 14.7 - - + +
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Residues in contact with LYS2382 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2366F LEU* 3.8 28.9 - - + +
2378F ALA 2.9 18.2 + - - +
2379F ALA* 3.3 8.9 + - - +
2381F VAL* 1.3 76.5 - - - +
2383F ALA* 1.3 67.8 + - - +
2385F LEU* 3.0 26.4 + - - +
2386F VAL 4.0 2.3 + - - -
2387F LEU* 4.1 25.3 + - + +
2388F LYS 5.8 4.9 - - - -
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Residues in contact with ALA2383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2379F ALA 3.0 16.5 + - - +
2380F GLN* 3.9 4.9 - - - +
2382F LYS* 1.3 76.4 - - - +
2384F PRO* 1.3 69.7 - - + +
2385F LEU 3.4 0.3 + - - -
2386F VAL* 3.7 9.7 + - - +
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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