Contacts of the helix formed by residues 982 - 987 (chain I) in PDB entry 3F5P
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 SER 982 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980I SER* 4.6 5.4 + - - -
981I PHE* 1.3 81.3 - - - +
983I ALA* 1.3 66.9 + - - +
984I ALA* 3.5 16.5 + - - +
985I ASP* 2.6 31.6 + - - +
986I VAL 4.1 0.3 + - - -
1044I ARG* 4.6 14.2 + - - -
1070I SER 4.5 3.3 + - - -
1072I GLY 5.0 5.7 + - - -
1075I THR* 4.9 1.4 + - - -
1243T GLU* 4.8 5.8 - - - -
1247T MET* 3.8 13.4 - - - +
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Residues in contact with ALA 983 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982I SER* 1.3 74.6 - - - +
984I ALA* 1.3 64.0 + - - +
985I ASP 2.9 1.6 + - - -
986I VAL 3.0 12.5 + - - -
987I TYR* 3.1 25.1 + - + +
1041I MET* 4.9 10.8 - - + +
1044I ARG* 4.0 21.5 - - + +
1045I ILE* 3.9 28.3 - - + -
1048I LEU* 4.2 4.5 - - + -
1247T MET* 3.9 14.7 - - + +
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Residues in contact with ALA 984 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982I SER* 3.5 9.5 + - - +
983I ALA* 1.3 77.4 - - - +
985I ASP* 1.3 57.9 + - - +
986I VAL 3.4 0.2 + - - -
987I TYR 4.3 0.4 - - - +
988I VAL* 2.8 34.5 + - + +
1044I ARG* 4.4 1.4 - - - +
1048I LEU* 3.8 17.2 - - + +
1070I SER* 3.3 32.5 - - - +
1075I THR* 3.8 26.9 - - + +
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Residues in contact with ASP 985 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980I SER 3.6 5.6 - - - +
981I PHE* 3.3 34.3 - - + -
982I SER* 2.6 45.8 + - - +
984I ALA* 1.3 79.0 - - - +
986I VAL* 1.3 56.1 + - - +
988I VAL* 4.2 8.3 - - - +
990I ASP* 4.5 10.9 - - - +
1070I SER 4.5 3.2 - - - +
1071I GLN* 2.2 40.1 + - - +
1264T SER* 5.8 0.5 - - - -
1265T SER* 3.5 15.4 + - - +
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Residues in contact with VAL 986 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981I PHE* 3.4 33.7 - - + -
982I SER 4.1 0.4 - - - +
983I ALA 3.0 2.9 + - - +
985I ASP* 1.3 74.3 - - - +
987I TYR* 1.3 86.4 + - + +
988I VAL 3.2 13.7 + - - +
1244T LEU* 4.8 3.8 - - + -
1247T MET* 3.5 18.6 - - + -
1257T PRO* 3.9 20.6 - - + -
1261T GLU* 3.4 32.4 - - + +
1262T ILE* 4.8 2.7 - - + +
1264T SER* 5.5 2.3 - - - -
1265T SER* 3.5 14.6 - - - +
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Residues in contact with TYR 987 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983I ALA* 3.1 24.8 + - + +
986I VAL* 1.3 105.4 - - + +
988I VAL* 1.3 63.1 + - - +
989I PRO* 4.7 0.2 - - - +
1045I ILE* 3.2 45.8 - - + +
1048I LEU* 4.2 22.4 - - + +
1049I ASN* 3.6 20.1 + - - +
1052I SER* 3.8 15.6 + - - -
1247T MET* 3.8 17.1 + - + +
1255T MET 2.7 23.6 + - - -
1256T ARG* 3.5 3.5 - - - -
1257T PRO* 3.0 30.0 - - + +
1261T GLU* 4.2 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