Contacts of the helix formed by residues 982 - 988 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1243D GLU* 5.4 2.5 - - - -
1247D MET* 3.9 13.8 - - - +
980G SER* 3.7 5.8 + - - -
981G PHE* 1.3 74.8 - - - +
983G ALA* 1.3 56.7 + - - +
984G ALA* 3.6 17.4 + - - +
985G ASP* 2.7 39.4 + - - +
986G VAL 4.0 0.3 + - - -
1041G MET* 5.9 0.4 - - - -
1044G ARG* 5.1 11.3 + - - -
1070G SER 4.5 4.3 + - - -
1072G GLY 5.2 4.5 + - - -
1075G THR* 4.9 3.3 + - - -
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Residues in contact with ALA 983 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247D MET* 3.9 14.2 - - + +
982G SER* 1.3 74.9 - - - +
984G ALA* 1.3 63.2 + - - +
985G ASP 3.0 1.0 + - - -
986G VAL 3.2 1.2 + - - -
987G TYR* 3.1 35.2 + - + +
1041G MET* 4.6 12.6 - - + +
1044G ARG* 4.3 12.3 - - + +
1045G ILE* 3.8 31.6 - - + -
1048G LEU* 3.8 9.9 - - + -
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Residues in contact with ALA 984 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982G SER* 3.1 11.0 + - - +
983G ALA* 1.3 78.8 - - - +
985G ASP* 1.3 57.4 + - - +
986G VAL 3.5 0.3 + - - -
987G TYR 4.3 0.2 - - - -
988G VAL* 2.9 32.9 + - + +
1044G ARG* 4.4 2.7 - - - +
1048G LEU* 3.5 17.0 - - + +
1070G SER* 3.5 26.5 - - - +
1075G THR* 3.8 29.8 - - + +
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Residues in contact with ASP 985 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1265D SER* 3.9 12.8 - - - -
980G SER 3.1 15.7 - - - +
981G PHE* 3.4 28.7 - - + -
982G SER* 2.7 38.3 + - - +
984G ALA* 1.3 80.9 - - - +
986G VAL* 1.3 56.6 + - - +
988G VAL* 4.3 8.2 - - - +
990G ASP* 4.8 9.7 - - - +
1070G SER* 4.6 2.2 - - - +
1071G GLN* 2.7 41.3 + - - +
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Residues in contact with VAL 986 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1244D LEU* 4.9 2.7 - - + -
1247D MET* 3.1 38.1 - - + -
1257D PRO* 3.9 29.4 - - + -
1261D GLU* 3.7 32.4 - - + +
1262D ILE* 4.5 2.9 - - + +
1264D SER* 5.9 0.5 - - - -
1265D SER* 3.9 19.5 - - - +
981G PHE* 4.3 11.0 - - + -
982G SER 4.1 2.5 - - - +
983G ALA 3.9 5.2 - - - +
985G ASP* 1.3 77.8 - - - +
987G TYR* 1.3 68.8 + - + +
988G VAL 3.4 5.8 + - - +
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Residues in contact with TYR 987 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247D MET* 3.4 25.1 + - - +
1255D MET 2.8 29.7 + - - -
1256D ARG* 3.6 3.6 - - - -
1257D PRO* 3.1 39.5 - - + +
1261D GLU* 4.4 18.4 - - - +
983G ALA* 3.1 31.9 + - + +
986G VAL* 1.3 81.0 - - + +
988G VAL* 1.3 61.8 + - - +
989G PRO* 4.0 3.8 - - - +
1045G ILE* 3.3 37.9 - - + +
1048G LEU* 4.2 19.2 - - + +
1049G ASN* 4.5 16.4 + - - +
1052G SER* 3.8 17.5 + - - -
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Residues in contact with VAL 988 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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984G ALA* 2.9 26.0 + - - +
985G ASP 4.3 8.7 - - - +
986G VAL 3.4 4.1 - - - +
987G TYR* 1.3 83.0 - - - +
989G PRO* 1.3 75.8 - - + +
990G ASP* 3.2 6.9 + - - +
992G TRP* 5.4 2.0 - - + -
993G GLU* 5.0 5.4 - - + +
1048G LEU* 3.8 31.9 - - + +
1051G ALA* 6.4 1.3 - - + -
1052G SER* 5.7 0.9 - - - +
1068G VAL* 4.3 27.6 - - + +
1070G SER* 3.8 20.0 - - - +
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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