Contacts of the helix formed by residues 1075 - 1084 (chain B) in PDB entry 1FP7
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 THR1075 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272B SO4 4.7 4.7 + - - -
1072B GLU* 4.7 1.7 + - - -
1073B GLY 3.2 1.4 + - - -
1074B LYS* 1.3 76.0 - - - +
1076B THR* 1.3 55.0 + - - +
1077B THR 3.2 2.0 - - - -
1078B SER* 2.3 40.2 + - - -
1079B VAL* 3.3 3.1 + - + -
1096B LEU* 4.5 12.6 - - + -
1097B ARG* 5.3 2.1 + - - -
1112B ALA 3.7 8.1 - - - +
1113B GLY* 3.1 33.2 - - - +
1301B GLU* 3.3 23.1 + - - +
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Residues in contact with THR1076 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073B GLY* 4.3 8.3 + - - -
1075B THR* 1.3 67.9 - - - +
1077B THR* 1.3 58.9 + - - +
1078B SER 2.5 1.0 + - - -
1079B VAL* 2.4 31.3 + - - +
1080B GLY 2.9 9.4 + - - -
1113B GLY* 2.4 37.2 + - - -
1114B GLY* 2.9 31.4 - - - +
1117B ALA* 3.9 9.2 - - + -
1382B ASN* 5.3 7.0 - - - +
1409B SER* 4.7 3.6 - - - -
1412B TRP* 4.2 29.5 - - + +
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Residues in contact with THR1077 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062B VAL* 4.3 9.0 - - + +
1073B GLY* 3.5 18.6 + - - -
1075B THR 2.9 1.2 + - - -
1076B THR* 1.3 78.3 - - - +
1078B SER* 1.3 59.7 + - - +
1079B VAL 3.4 0.2 - - - -
1080B GLY* 4.2 4.5 - - - +
1081B LEU* 3.5 19.8 + - - +
1329B VAL* 5.6 0.2 - - + -
1331B VAL* 3.5 34.3 - - + +
1380B ALA* 4.3 14.6 - - + -
1381B ILE 5.9 0.2 - - - -
1382B ASN* 4.2 18.4 + - - +
1407B ALA* 5.1 11.2 + - + +
1409B SER* 5.2 7.8 + - - -
1422B LEU* 5.1 8.0 - - + +
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Residues in contact with SER1078 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062B VAL* 3.3 26.5 - - - +
1074B LYS 2.4 30.7 + - - -
1075B THR 2.3 29.3 + - - -
1076B THR 2.5 0.2 + - - -
1077B THR* 1.3 68.5 - - - +
1079B VAL* 1.3 59.4 + - - -
1081B LEU* 3.7 4.4 - - - +
1082B THR* 3.5 5.5 + - - -
1094B VAL* 4.0 2.3 - - - +
1096B LEU* 4.8 9.0 - - - -
1299B VAL* 3.2 24.6 - - - +
1300B THR 4.5 1.8 - - - -
1301B GLU* 2.6 18.6 + - - -
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Residues in contact with VAL1079 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075B THR* 4.4 11.9 - - + +
1076B THR* 2.4 17.6 + - - +
1078B SER* 1.3 69.4 - - - +
1080B GLY* 1.3 52.9 + - - +
1081B LEU 2.8 4.7 - - - -
1082B THR* 2.4 36.5 + - - -
1083B ASP* 3.0 24.5 + - - +
1094B VAL* 4.5 6.5 - - + -
1096B LEU* 4.3 24.2 - - + -
1113B GLY* 4.9 1.3 - - - -
1117B ALA* 2.7 49.4 - - + +
1119B VAL* 4.6 6.3 - - + -
1262B THR* 3.9 8.5 - - + +
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Residues in contact with GLY1080 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076B THR 2.9 10.5 + - - -
1077B THR 4.7 0.7 - - - -
1079B VAL* 1.3 76.7 - - - +
1081B LEU* 1.3 55.9 + - - +
1082B THR 3.1 0.2 - - - -
1083B ASP* 3.8 9.2 - - - -
1084B ALA* 2.9 30.7 + - - +
1116B TYR 5.3 0.7 - - - -
1117B ALA* 3.8 7.2 - - - +
1409B SER* 3.4 34.3 + - - -
1415B GLY 5.0 2.5 - - - -
1416B GLY* 4.1 2.6 - - - -
1419B GLY* 4.8 1.3 - - - -
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Residues in contact with LEU1081 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060B ILE* 3.9 28.7 - - + +
1062B VAL* 5.2 4.0 - - + -
1077B THR 3.5 20.5 + - - +
1078B SER 3.7 6.5 - - - +
1079B VAL 2.8 1.0 + - - -
1080B GLY* 1.3 75.7 - - - +
1082B THR* 1.3 58.2 + - - +
1084B ALA* 4.2 2.2 - - - -
1085B LEU* 2.8 31.3 + - + +
1299B VAL* 4.0 17.4 - - + +
1329B VAL* 4.5 13.5 - - + -
1419B GLY* 4.7 2.7 - - - +
1422B LEU* 4.0 16.4 - - + -
1423B ALA* 3.8 29.6 - - + +
1426B VAL* 3.9 15.0 - - + -
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Residues in contact with THR1082 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078B SER 3.5 5.9 + - - -
1079B VAL* 2.4 28.1 + - - -
1081B LEU* 1.3 67.1 - - - +
1083B ASP* 1.3 56.9 + - - +
1084B ALA 2.9 4.3 - - - -
1085B LEU* 3.8 4.0 - - - -
1086B ALA* 3.0 30.3 + - - +
1092B VAL* 4.0 11.7 - - + -
1093B MET 4.3 5.6 - - - +
1094B VAL* 2.9 38.9 - - + +
1262B THR* 5.3 0.4 - - - +
1266B THR* 3.2 36.0 - - + +
1299B VAL* 3.6 10.3 - - - +
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Residues in contact with ASP1083 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079B VAL* 3.0 18.7 + - - +
1080B GLY* 4.2 2.5 - - - +
1082B THR* 1.3 77.3 - - - +
1084B ALA* 1.3 56.6 + - - +
1087B ARG* 2.8 34.3 - - - +
1116B TYR 3.2 15.8 - - - +
1262B THR* 3.2 26.5 + - - +
1264B GLU* 2.9 41.7 - - - +
1266B THR* 3.1 19.6 + - - -
1416B GLY* 3.2 10.5 - - - +
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Residues in contact with ALA1084 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080B GLY 2.9 19.5 + - - +
1081B LEU* 4.2 1.6 - - - -
1082B THR 2.9 0.2 - - - -
1083B ASP* 1.3 79.9 - - - +
1085B LEU* 1.3 68.8 + - - +
1087B ARG* 3.2 15.7 + - - +
1088B LEU* 3.7 12.0 - - - +
1416B GLY 3.2 20.6 - - - +
1419B GLY 3.3 23.8 - - - +
1420B LEU* 3.9 5.4 - - - +
1423B ALA* 3.8 9.0 - - + -
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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