Contacts of the helix formed by residues 1118 - 1131 (chain G) in PDB entry 1F2I
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 ARG1118 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1006A C 3.5 30.4 - - - +
1007A G 2.7 47.3 + - - -
2008B C 3.9 2.4 - - - +
1105G TYR* 3.7 7.2 - - - -
1116G PHE* 3.7 6.4 - - - +
1117G SER* 1.3 82.9 - - - +
1119G SER* 1.3 61.9 + - - +
1120G ASP* 2.7 36.9 + - - +
1121G GLU* 3.2 37.6 + - - +
1122G LEU 3.4 4.5 + - - -
2118H ARG* 3.5 51.8 - - + +
2119H SER* 5.7 2.2 - - - +
2120H ASP* 4.4 7.1 + - - -
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Residues in contact with SER1119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1105G TYR* 3.3 41.5 - - - -
1118G ARG* 1.3 69.9 - - - +
1120G ASP* 1.3 67.2 + - - +
1121G GLU 3.1 2.0 - - - -
1122G LEU* 3.2 4.2 + - - +
1123G THR* 3.1 24.9 + - - -
2099H VAL* 3.8 16.8 + - - +
2100H PRO 5.5 0.2 + - - -
2117H SER* 5.4 2.2 + - - -
2118H ARG* 5.5 2.2 - - - +
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Residues in contact with ASP1120 (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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1006A C 3.9 10.2 + - - +
2006B C 6.4 0.2 - - - -
2007B G 4.8 16.1 - - + +
2008B C 4.3 5.0 + - - -
1118G ARG* 2.7 53.2 + - - +
1119G SER* 1.3 75.7 + - - +
1121G GLU* 1.3 61.7 + - - +
1123G THR* 3.5 8.1 + - - -
1124G ARG* 3.2 31.7 + - + +
2118H ARG* 4.2 12.0 + - - -
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Residues in contact with GLU1121 (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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1004A G 4.5 4.1 + - + -
1005A G 3.3 42.3 + - + +
1006A C 3.3 34.3 + - + +
1116G PHE* 3.6 22.5 - - + +
1117G SER* 3.4 14.4 + - - -
1118G ARG* 3.2 37.2 + - + +
1119G SER 3.1 0.4 - - - -
1120G ASP* 1.3 76.9 - - - +
1122G LEU* 1.3 64.7 + - - +
1124G ARG* 3.4 11.5 + - - +
1125G HIS* 3.2 21.1 + - - +
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Residues in contact with LEU1122 (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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1105G TYR* 3.9 22.9 - - + -
1106G ALA 3.8 16.8 - - - +
1107G CYS* 3.7 25.4 - - + +
1108G PRO* 4.5 1.3 - - + -
1116G PHE* 3.8 27.3 - - + -
1118G ARG 3.4 1.8 + - - -
1119G SER 3.2 7.5 + - - +
1121G GLU* 1.3 80.1 - - - +
1123G THR* 1.3 64.3 + - - +
1125G HIS* 3.0 3.8 + - + +
1126G ILE* 2.9 41.5 + - + +
2097H TYR* 5.2 2.7 - - + +
2099H VAL* 3.5 35.0 - - + -
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Residues in contact with THR1123 (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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1119G SER* 3.1 16.4 + - - -
1120G ASP* 3.6 12.2 - - - -
1121G GLU 3.3 0.2 - - - -
1122G LEU* 1.3 77.0 - - - +
1124G ARG* 1.3 60.8 + - + +
1126G ILE* 3.8 12.8 + - - +
1127G ARG* 3.8 35.2 + - - +
2099H VAL* 3.4 22.0 + - + +
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Residues in contact with ARG1124 (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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1003A G 5.5 4.1 + - + +
1004A G 4.6 6.4 + - - +
1005A G 2.7 36.6 + - - -
1006A C 3.2 12.5 - - - +
2008B C 6.0 0.8 - - - -
2009B G 3.1 21.2 + - - -
1120G ASP* 3.2 19.0 + - + +
1121G GLU* 3.6 10.7 - - - +
1122G LEU 3.2 0.6 - - - -
1123G THR* 1.3 74.7 - - - +
1125G HIS* 1.3 66.2 + - - +
1127G ARG* 3.1 42.5 + - - +
1128G ILE* 4.0 4.4 + - - +
1145G SER* 5.8 0.3 - - - -
1146G ARG* 3.5 52.3 - - - +
1147G SER* 5.5 2.2 - - - +
1148G ASP* 3.9 12.9 + - - +
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Residues in contact with HIS1125 (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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1004A G 2.7 33.3 + - - +
1107G CYS* 3.6 9.6 - - + -
1112G CYS* 3.6 1.3 - - - -
1114G ARG* 3.5 25.4 - - + +
1116G PHE* 3.4 30.9 - + + -
1121G GLU 3.2 3.8 + - - +
1122G LEU* 3.0 8.7 + - + +
1124G ARG* 1.3 74.8 - - - +
1126G ILE* 1.3 63.0 + - - +
1127G ARG 3.0 2.2 - - - -
1128G ILE* 2.8 42.4 + - + +
1129G HIS* 2.9 11.4 + + - -
1201G ZN 2.1 36.9 - - - -
6096L ASN* 5.6 2.2 - - - -
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Residues in contact with ILE1126 (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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1107G CYS* 4.7 1.6 - - - -
1108G PRO* 3.6 33.4 - - + -
1122G LEU* 2.9 39.4 + - + +
1123G THR* 3.9 8.3 - - - +
1124G ARG 3.3 0.2 - - - -
1125G HIS* 1.3 81.4 - - + +
1127G ARG* 1.3 61.6 + - + +
1128G ILE 3.0 0.2 - - - -
1129G HIS* 3.1 20.4 + - + +
1130G THR* 3.1 26.0 + - + +
2094H LEU* 4.4 17.0 - - + +
2097H TYR* 3.7 25.6 - - + +
2099H VAL* 4.2 6.7 - - + -
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Residues in contact with ARG1127 (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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1003A G 5.2 2.4 + - - +
1123G THR* 3.8 31.6 + - - +
1124G ARG* 3.1 42.9 + - - +
1125G HIS 3.0 0.6 - - - -
1126G ILE* 1.3 76.0 - - + +
1128G ILE* 1.3 59.1 + - - +
1129G HIS 3.3 0.2 - - - -
1130G THR* 3.4 8.7 - - - +
1131G GLY* 2.9 27.2 + - - -
1132G GLN* 3.5 33.7 + - + +
1134G PRO* 3.6 17.8 - - - +
1135G PHE* 4.1 19.8 - - - -
1145G SER* 2.8 36.9 + - - -
1146G ARG* 4.6 1.2 - - - +
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Residues in contact with ILE1128 (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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1003A G 3.5 62.1 - - - +
1004A G 3.6 11.9 - - - +
1124G ARG 4.5 1.8 - - - +
1125G HIS* 2.8 28.8 + - + +
1127G ARG* 1.3 80.1 - - - +
1129G HIS* 1.3 73.7 + - + +
1131G GLY* 3.9 5.5 + - - -
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Residues in contact with HIS1129 (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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1107G CYS* 3.6 11.9 - - - -
1109G VAL* 3.8 16.5 - - + +
1112G CYS* 4.1 10.7 - - + +
1125G HIS* 2.9 17.9 + + - -
1126G ILE* 3.1 14.1 + - + +
1128G ILE* 1.3 88.6 - - + +
1130G THR* 1.3 61.6 + - - +
1131G GLY 3.5 0.2 + - - -
1201G ZN 2.1 37.3 - - - -
2094H LEU* 3.9 18.2 - - + +
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Residues in contact with THR1130 (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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1126G ILE* 3.1 18.7 + - + +
1127G ARG* 3.4 11.6 - - - +
1129G HIS* 1.3 75.3 - - - +
1131G GLY* 1.3 63.7 + - - +
1132G GLN* 3.2 39.2 + - - +
2094H LEU* 3.7 38.1 - - + +
2095H LEU* 3.7 20.3 - - + +
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Residues in contact with GLY1131 (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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1127G ARG 2.9 13.0 + - - -
1128G ILE 3.9 4.8 + - - -
1129G HIS 3.3 3.6 - - - -
1130G THR* 1.3 77.9 - - - +
1132G GLN* 1.3 63.3 + - - +
1133G LYS* 3.7 14.4 + - - +
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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