Contacts of the helix formed by residues 1098 - 1113 (chain C) in PDB entry 5MBV
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 THR1098 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1096C GLN* 3.5 12.7 + - + +
1097C LEU* 1.3 73.3 - - - +
1099C PRO* 1.3 69.2 - - + +
1100C GLU* 4.2 6.5 - - - +
1101C THR* 2.7 39.8 + - - +
1102C MET* 3.0 28.8 + - - +
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Residues in contact with PRO1099 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068C ARG* 5.1 14.3 + - - +
1097C LEU 4.6 1.6 - - - +
1098C THR* 1.3 85.6 - - + +
1100C GLU* 1.3 60.1 + - + +
1102C MET* 3.6 14.0 - - + +
1103C GLU* 3.0 37.9 + - - +
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Residues in contact with GLU1100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098C THR* 3.2 6.8 - - - +
1099C PRO* 1.3 82.9 - - + +
1101C THR* 1.3 63.8 + - + +
1103C GLU* 3.3 21.6 + - - +
1104C ALA* 3.2 19.2 + - - +
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Residues in contact with THR1101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819C GLU* 6.1 1.3 - - - +
1036C LEU* 5.1 5.8 - - + +
1094C TRP* 5.0 22.0 - - + +
1097C LEU* 3.5 14.3 - - - +
1098C THR* 2.7 31.6 + - - +
1100C GLU* 1.3 79.0 - - + +
1102C MET* 1.3 59.7 + - - +
1104C ALA* 3.2 8.6 + - + +
1105C ILE* 3.0 34.7 + - - +
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Residues in contact with MET1102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068C ARG* 4.0 38.4 - - - +
1071C PHE* 3.8 25.9 - - + -
1072C LEU* 4.1 20.6 - - + -
1097C LEU* 3.8 35.2 - - + +
1098C THR 3.0 16.6 + - - +
1099C PRO* 3.6 12.1 - - + +
1100C GLU 3.3 0.2 - - - -
1101C THR* 1.3 79.3 + - - +
1103C GLU* 1.3 60.9 + - - +
1105C ILE* 3.6 8.1 + - - +
1106C VAL* 3.1 27.0 + - + +
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Residues in contact with GLU1103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068C ARG* 4.4 20.5 + - - +
1099C PRO* 3.0 21.9 + - - +
1100C GLU* 3.6 23.4 - - - +
1101C THR 3.2 0.2 - - - -
1102C MET* 1.3 75.7 - - - +
1104C ALA* 1.3 59.3 + - - +
1106C VAL* 3.1 8.4 + - - +
1107C GLU* 2.8 44.9 + - + +
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Residues in contact with ALA1104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036C LEU* 5.2 9.2 - - + -
1100C GLU 3.2 13.4 + - - +
1101C THR* 3.2 12.7 + - + +
1103C GLU* 1.3 75.6 - - - +
1105C ILE* 1.3 63.7 + - + +
1107C GLU* 4.0 10.2 - - - +
1108C GLN* 3.1 34.3 + - + +
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Residues in contact with ILE1105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036C LEU* 3.7 29.2 - - + +
1038C LEU* 3.7 44.0 - - + +
1042C GLY* 5.3 0.2 - - - -
1071C PHE* 4.2 20.4 - - + -
1075C TYR* 5.8 0.4 - - + -
1094C TRP* 3.6 33.7 - - + -
1097C LEU* 4.7 7.4 - - + -
1101C THR 3.0 23.4 + - - +
1102C MET* 3.9 6.5 - - - +
1104C ALA* 1.3 73.6 - - - +
1106C VAL* 1.3 55.2 + - - +
1108C GLN* 3.9 0.7 - - - +
1109C SER* 2.7 38.6 + - - +
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Residues in contact with VAL1106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045C TRP* 3.5 62.7 - - + +
1068C ARG* 6.3 0.7 - - - +
1071C PHE* 4.5 14.6 - - + -
1102C MET* 3.1 20.7 + - + +
1103C GLU* 3.1 13.6 + - - +
1105C ILE* 1.3 77.4 - - - +
1107C GLU* 1.3 60.5 + - + +
1109C SER* 2.9 7.0 + - - +
1110C GLN* 2.8 31.8 + - - +
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Residues in contact with GLU1107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103C GLU* 2.8 30.2 + - + +
1104C ALA* 4.0 8.2 - - - +
1106C VAL* 1.3 81.1 - - + +
1108C GLN* 1.3 69.2 + - - +
1110C GLN* 3.3 14.2 + - - +
1111C ARG* 3.3 19.4 + - - +
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Residues in contact with GLN1108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029C GLU* 5.6 4.8 + - - +
1035C LEU* 3.4 26.5 - - + +
1036C LEU* 3.3 25.4 - - + +
1037C VAL* 4.1 2.2 - - + -
1104C ALA* 3.1 19.2 + - + +
1107C GLU* 1.3 83.9 - - - +
1109C SER* 1.3 61.3 + - - +
1111C ARG* 3.3 23.0 + - - +
1112C PHE* 3.3 33.4 + - - -
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Residues in contact with SER1109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037C VAL* 4.3 11.1 - - - +
1038C LEU 4.7 3.1 - - - -
1042C GLY* 3.9 25.0 + - - -
1045C TRP* 5.4 2.4 - - - -
1046C LEU* 4.0 4.2 - - - +
1105C ILE 2.7 23.3 + - - -
1106C VAL* 2.9 16.6 + - - +
1108C GLN* 1.3 73.9 - - - +
1110C GLN* 1.3 63.5 + - - +
1111C ARG 3.1 0.2 - - - -
1113C LEU* 3.1 52.8 + - - +
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Residues in contact with GLN1110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045C TRP* 4.3 16.9 - - + -
1046C LEU* 4.4 13.7 - - + -
1057C MET* 3.3 42.5 - - + +
1106C VAL* 2.8 20.6 + - - +
1107C GLU* 3.4 15.3 - - - +
1109C SER* 1.3 77.3 + - - +
1111C ARG* 1.3 57.1 + - - +
1114C LEU* 3.2 28.0 - - + +
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Residues in contact with ARG1111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1022C GLN* 3.2 34.1 + - - +
1025C GLU* 4.8 17.0 - - - +
1029C GLU* 5.8 3.8 - - - +
1107C GLU 3.3 10.2 + - - +
1108C GLN* 3.3 23.0 + - - +
1109C SER 3.1 0.6 - - - -
1110C GLN* 1.3 80.0 - - - +
1112C PHE* 1.3 102.6 + - + +
1114C LEU* 3.7 5.9 + - - +
1115C PRO* 3.9 6.2 - - - +
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Residues in contact with PHE1112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841C TRP* 3.4 28.3 - + + -
978C MET* 4.6 7.1 - - + +
981C TRP* 5.6 0.7 + - - -
1022C GLN* 3.5 37.5 - - + +
1023C LEU* 4.8 9.4 - - + +
1026C GLY* 3.6 24.2 - - - -
1029C GLU* 5.3 3.6 - - + -
1035C LEU* 3.6 29.8 - - + -
1037C VAL* 3.9 12.8 - - + -
1108C GLN* 3.3 27.6 + - - +
1111C ARG* 1.3 110.6 - - + +
1113C LEU* 1.3 66.0 + - + +
1114C LEU 3.2 0.9 - - - -
1115C PRO* 3.2 22.7 - - - +
1116C LEU* 4.9 0.9 + - - +
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Residues in contact with LEU1113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841C TRP* 5.8 1.1 - - + -
974C VAL* 5.1 2.2 - - + -
978C MET* 3.7 27.1 - - + -
1037C VAL* 3.8 21.3 - - + -
1038C LEU 3.8 18.2 - - - +
1039C PRO* 4.2 14.4 - - + +
1042C GLY 4.2 0.7 - - - -
1043C GLY* 4.1 13.7 - - - +
1046C LEU* 3.3 16.7 - - + +
1109C SER* 3.1 35.1 + - - +
1112C PHE* 1.3 76.2 - - + +
1114C LEU* 1.3 62.9 + - - +
1115C PRO* 3.6 0.9 - - - -
1116C LEU* 3.3 32.5 - - + +
1117C PHE* 3.4 7.0 - - + -
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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