Contacts of the helix formed by residues 1098 - 1102 (chain A) in PDB entry 5FLM
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 PRO1098 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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529A GLN* 3.2 18.2 - - - +
1094A SER 3.1 21.1 - - - +
1095A LEU 3.7 8.1 - - - +
1097A GLU* 1.3 91.2 - - - +
1099A ALA* 1.3 54.7 + - - +
1101A GLN* 2.7 35.9 + - + +
1102A MET* 3.1 20.2 + - + +
1386A ILE* 5.1 6.5 - - + +
1391A SER* 4.4 17.5 - - - +
1393A VAL* 3.6 19.3 - - + -
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Residues in contact with ALA1099 (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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853A LYS* 5.9 0.2 - - - +
857A THR* 3.1 30.2 - - + +
860A ILE* 5.4 3.8 - - + -
1095A LEU 4.0 4.6 + - - +
1096A GLY* 3.3 19.2 + - - +
1097A GLU 3.1 1.2 - - - -
1098A PRO* 1.3 78.1 - - - +
1100A THR* 1.3 60.5 + - - +
1102A MET* 3.2 22.4 + - - -
1121A VAL* 3.5 11.0 - - + +
1124A LEU* 4.0 26.0 - - + -
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Residues in contact with THR1100 (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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464A LEU* 3.9 39.9 - - + +
853A LYS* 3.7 28.6 + - - +
854A THR* 6.6 0.4 - - - -
857A THR* 3.7 30.7 - - - +
858A GLY 5.3 0.4 - - - +
861A GLN* 6.5 0.9 - - + -
1096A GLY 4.3 6.5 - - - +
1097A GLU* 2.7 22.4 + - - +
1099A ALA* 1.3 76.1 - - - +
1101A GLN* 1.3 65.4 + - - +
1102A MET 3.4 0.6 + - - -
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Residues in contact with GLN1101 (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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493A ASN* 5.5 7.1 - - - +
853A LYS* 4.9 3.4 - - - +
1097A GLU* 4.7 15.9 + - - +
1098A PRO* 2.7 24.3 + - + +
1100A THR* 1.3 79.3 + - - +
1102A MET* 1.3 54.1 + - - -
1103A THR* 3.2 11.0 + - - -
1104A LEU* 4.1 4.2 + - - -
1389A ASP* 4.0 7.3 - - - +
1391A SER* 5.7 3.1 + - - -
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Residues in contact with MET1102 (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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1095A LEU 5.5 1.6 - - - +
1098A PRO* 3.1 18.6 - - + +
1099A ALA* 3.2 34.8 + - - +
1100A THR 3.4 0.2 - - - -
1101A GLN* 1.3 75.8 - - - +
1103A THR* 1.3 61.0 + - - +
1104A LEU* 2.9 11.5 + - - +
1120A GLY* 3.6 45.3 - - - +
1121A VAL* 4.1 11.5 + - + -
1124A LEU* 4.5 12.6 - - + -
1385A VAL* 3.5 38.6 - - + +
1386A ILE* 4.6 14.6 - - + +
1389A ASP* 3.4 16.9 - - - +
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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