Contacts of the strand formed by residues 1399 - 1404 (chain F) in PDB entry 6C3P
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 GLU1399 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1348F ASN* 4.4 2.0 - - + +
1349F LEU 4.2 0.2 - - - -
1350F SER* 3.1 41.8 + - - +
1397F THR* 3.4 8.5 + - - +
1398F PHE* 1.3 104.4 - - + +
1400F GLY* 1.3 71.0 + - - +
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Residues in contact with GLY1400 (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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1347F GLN 3.8 6.3 - - - -
1348F ASN* 3.2 23.0 + - - +
1349F LEU* 4.1 3.1 - - - -
1397F THR* 4.0 7.1 + - - +
1398F PHE 5.1 0.3 - - - +
1399F GLU* 1.3 85.8 + - - +
1401F HIS* 1.3 69.8 + - - +
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Residues in contact with HIS1401 (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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1345F GLN 4.5 1.1 - - - +
1346F ILE* 3.9 0.9 - - - -
1347F GLN* 2.9 67.9 + - + +
1349F LEU* 4.2 13.1 - - - +
1397F THR* 5.2 0.9 - - - -
1400F GLY* 1.3 78.6 - - - +
1402F ILE* 1.3 60.5 + - - +
1403F ILE* 3.8 31.4 - - + +
1408F ASP* 3.4 22.2 - - - +
1409F ILE* 5.5 3.1 - - + -
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Residues in contact with ILE1402 (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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1344F ILE* 3.7 22.2 - - + -
1345F GLN 4.0 2.5 - - - -
1346F ILE* 3.6 20.9 - - + +
1349F LEU* 4.5 13.2 - - + +
1390F ALA 4.8 9.0 - - - +
1391F PHE* 3.6 39.5 - - + +
1401F HIS* 1.3 74.9 - - - +
1403F ILE* 1.3 69.3 + - - +
1404F ILE* 4.1 8.5 + - + -
1408F ASP* 2.9 19.9 + - - +
1409F ILE* 3.1 47.2 + - + +
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Residues in contact with ILE1403 (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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1343F LYS 3.7 0.5 - - - +
1344F ILE* 3.5 8.7 - - - +
1345F GLN* 3.1 43.4 + - + +
1401F HIS* 3.8 27.1 - - + +
1402F ILE* 1.3 73.4 - - - +
1404F ILE* 1.3 70.5 + - - +
1405F ASP* 4.8 1.1 - - - -
1406F GLY 4.2 7.4 - - - +
1407F ILE* 2.9 19.5 - - - +
1408F ASP* 3.4 28.9 - - + +
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Residues in contact with ILE1404 (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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1338F TRP* 3.3 33.2 - - + -
1339F PRO* 5.0 7.2 - - + -
1342F GLY* 5.2 5.2 - - - -
1343F LYS 3.9 4.9 - - - +
1344F ILE* 4.9 14.8 - - + -
1391F PHE* 6.4 1.1 - - + -
1402F ILE* 4.4 17.9 - - + -
1403F ILE* 1.3 79.2 - - - +
1405F ASP* 1.3 65.9 + - - +
1406F GLY 2.9 0.7 + - - -
1407F ILE* 2.6 39.0 + - - +
1408F ASP 4.2 9.2 - - - +
1409F ILE* 3.5 31.9 - - + -
1412F LEU* 5.4 2.7 - - + -
1421F LEU* 5.7 11.0 - - + -
1501F ILE* 5.4 7.9 - - + -
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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