Contacts of the strand formed by residues 1342 - 1346 (chain A) in PDB entry 1FNF
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 SER1342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1337A ASP 4.2 1.8 + - - -
1338A ILE* 3.7 0.2 - - - -
1339A THR* 2.8 52.6 + - - +
1340A ALA 3.8 0.8 - - - -
1341A ASN* 1.3 85.0 + - - +
1343A PHE* 1.3 66.0 + - - +
1383A THR* 4.7 6.8 - - - +
1384A LEU 3.0 20.4 - - - -
1385A THR* 4.0 13.0 - - - -
1387A LEU* 3.8 7.5 - - - +
1415A THR* 4.1 1.5 - - - +
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Residues in contact with PHE1343 (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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1335A PHE* 3.7 20.9 - + - -
1336A SER 3.7 0.2 - - - +
1337A ASP 3.6 10.8 - - - -
1338A ILE* 3.7 23.8 - - + -
1342A SER* 1.3 80.3 + - - +
1344A THR* 1.3 62.8 + - - +
1345A VAL* 3.6 22.8 + - + -
1382A ILE 3.9 0.2 - - - +
1383A THR* 4.2 2.5 - - - -
1384A LEU* 2.8 38.1 + - + -
1387A LEU* 3.4 30.7 - - + -
1393A TYR* 4.0 14.4 - + + -
1395A VAL* 4.0 13.0 - - + -
1413A GLN* 3.6 37.2 - - + -
1414A SER 4.8 2.2 - - - -
1415A THR* 3.9 9.4 - - + -
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Residues in contact with THR1344 (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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1335A PHE* 3.1 7.4 - - - +
1336A SER* 2.8 43.2 + - - -
1337A ASP* 2.9 30.8 + - - +
1343A PHE* 1.3 72.0 - - - +
1345A VAL* 1.3 66.4 + - - +
1346A HIS* 3.4 19.8 - - + +
1381A SER* 4.3 9.0 - - - +
1382A ILE* 3.2 13.5 - - - +
1383A THR* 2.9 26.6 + - - +
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Residues in contact with VAL1345 (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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1333A ILE* 4.0 21.1 - - + -
1334A ASP 3.7 2.9 - - - -
1335A PHE* 4.2 7.4 - - + -
1343A PHE* 3.6 30.7 - - + -
1344A THR* 1.3 72.7 - - - +
1346A HIS* 1.3 56.3 + - - +
1347A TRP* 3.7 4.4 - - + -
1381A SER* 2.8 14.4 - - - -
1382A ILE* 2.6 48.2 + - + +
1384A LEU* 4.0 17.7 - - + -
1395A VAL* 3.9 23.3 - - + -
1397A ILE* 4.0 11.7 - - + -
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Residues in contact with HIS1346 (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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1332A GLY 4.4 1.1 - - - -
1333A ILE* 3.2 8.5 - - - +
1334A ASP* 2.7 66.7 + - + +
1335A PHE 4.1 0.4 - - - -
1336A SER* 2.6 39.0 + - - -
1344A THR* 3.4 23.6 + - + +
1345A VAL* 1.3 72.5 - - - +
1347A TRP* 1.3 64.6 + - - +
1380A ASN* 3.3 10.1 - - - +
1381A SER* 3.8 17.9 - - - -
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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