Contacts of the helix formed by residues 1031 - 1039 (chain N) in PDB entry 2O5J
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 ASN1031 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1024N ALA* 5.5 0.4 - - - -
1030N GLY* 1.3 75.3 - - - +
1032N PRO* 1.3 66.9 - - - +
1033N GLN* 3.0 16.0 + - - +
1034N GLN* 2.6 81.1 + - - +
1035N ILE* 2.9 17.3 + - - +
1037N GLN* 5.3 0.2 + - - -
1244N GLY* 6.1 0.3 - - - -
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Residues in contact with PRO1032 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004N THR* 5.1 13.8 - - + +
1008N PHE* 4.7 24.9 - - + -
1024N ALA* 5.6 4.7 - - + +
1030N GLY 4.4 3.1 - - - +
1031N ASN* 1.3 89.1 - - + +
1033N GLN* 1.3 61.9 + - - +
1034N GLN 3.4 0.2 + - - -
1035N ILE* 3.7 7.4 + - + +
1036N ARG* 3.4 20.1 + - - +
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Residues in contact with GLN1033 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000N THR* 5.1 2.2 + - - -
1031N ASN* 3.0 15.6 + - - +
1032N PRO* 1.3 78.5 - - - +
1034N GLN* 1.3 58.3 + - - +
1036N ARG* 2.7 57.7 + - - +
1037N GLN* 3.0 25.5 + - - +
1244N GLY* 4.2 13.0 - - - +
1245N GLY* 5.7 2.4 - - - -
1246N VAL 5.8 2.2 + - - -
1247N ALA* 5.8 3.6 - - - +
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Residues in contact with GLN1034 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877M PRO 4.4 7.0 - - - +
878M SER* 2.8 41.3 - - - +
880M MET* 3.9 17.0 - - + -
1031N ASN* 2.6 45.5 + - + +
1033N GLN* 1.3 70.4 - - - +
1035N ILE* 1.3 59.0 + - + +
1036N ARG 3.0 1.3 - - - -
1037N GLN* 2.8 35.0 + - - +
1038N LEU* 3.4 11.5 - - - +
1243N THR* 3.0 47.9 + - - +
1244N GLY* 4.8 1.2 - - - -
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Residues in contact with ILE1035 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877M PRO* 5.1 10.1 - - + +
1007N VAL* 5.2 3.6 - - + -
1008N PHE* 4.8 17.3 - - + -
1011N PHE* 4.8 7.0 - - + -
1020N LEU* 3.4 51.1 - - + +
1024N ALA* 4.5 18.6 - - + -
1030N GLY* 4.7 5.6 - - - -
1031N ASN 2.9 32.0 + - - +
1032N PRO* 4.1 7.0 - - + +
1034N GLN* 1.3 73.1 - - + +
1036N ARG* 1.3 61.3 + - - +
1038N LEU* 3.1 13.1 + - + +
1039N CYS* 3.1 27.3 + - + +
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Residues in contact with ARG1036 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000N THR* 3.3 20.4 + - - -
1003N VAL* 4.1 12.1 - - + -
1004N THR* 3.3 34.1 - - + +
1007N VAL* 5.5 4.0 - - + -
1032N PRO 3.4 12.2 + - - +
1033N GLN* 2.7 64.0 + - - +
1034N GLN 3.0 0.8 + - - -
1035N ILE* 1.3 79.6 - - - +
1037N GLN* 1.3 56.2 + - - +
1040N GLY* 2.8 16.0 + - - +
1041N LEU 2.7 49.2 + - - +
1042N ARG* 2.9 34.9 - - - +
1043N GLY 3.5 6.1 - - - +
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Residues in contact with GLN1037 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880M MET* 3.5 27.0 - - - +
1031N ASN* 5.3 0.2 + - - -
1033N GLN* 3.0 29.6 + - - +
1034N GLN* 2.8 17.8 + - - +
1036N ARG* 1.3 82.5 - - - +
1038N LEU* 1.3 64.0 + - + +
1042N ARG* 3.1 53.3 + - + +
1060N SER* 3.5 6.3 - - - -
1061N PHE* 2.8 31.2 + - + -
1244N GLY* 3.6 26.5 + - - +
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Residues in contact with LEU1038 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877M PRO* 4.6 18.8 - - + +
879M ARG 5.8 0.2 - - - +
880M MET* 4.3 15.7 - - + -
882M LEU* 3.9 32.8 - - + -
954N ALA* 5.1 2.5 - - + -
1020N LEU* 4.1 24.7 - - + -
1034N GLN 3.4 18.4 - - - +
1035N ILE* 3.7 11.2 - - + +
1036N ARG 3.1 0.4 - - - -
1037N GLN* 1.3 83.3 - - + +
1039N CYS* 1.3 63.0 + - + +
1060N SER* 3.1 18.0 - - - -
1061N PHE* 3.8 28.3 - - + +
1062N ARG* 3.2 19.8 + - - +
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Residues in contact with CYS1039 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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954N ALA* 3.0 52.0 - - - -
955N VAL 3.0 24.5 - - - +
956N ILE* 3.3 32.8 - - - +
957N PRO* 4.9 0.9 - - - -
960N LYS* 4.5 0.7 - - - +
1007N VAL* 4.2 12.8 - - + -
1011N PHE* 5.0 2.0 - - - -
1020N LEU* 5.3 2.0 - - - -
1035N ILE* 3.1 15.5 + - + +
1038N LEU* 1.3 74.0 - - + +
1040N GLY* 1.3 71.6 + - - +
1060N SER* 3.7 2.8 + - - -
1062N ARG* 4.9 0.2 - - - -
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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