Contacts of the helix formed by residues 1031 - 1040 (chain D) in PDB entry 4OIP
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1008D PHE* 4.9 1.6 - - - -
1024D ALA* 5.2 2.5 - - - -
1030D GLY* 1.3 74.5 - - - -
1032D PRO* 1.3 76.5 - - + +
1033D GLN* 3.1 11.1 + - - +
1034D GLN* 2.9 59.9 + - - +
1035D ILE* 3.2 23.6 + - - +
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Residues in contact with PRO1032 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004D THR* 4.2 12.5 - - + +
1008D PHE* 3.5 32.8 - - + -
1024D ALA* 6.2 0.4 - - + -
1031D ASN* 1.3 90.6 - - + +
1033D GLN* 1.3 61.6 + - + +
1035D ILE* 3.6 2.4 + - - +
1036D ARG* 2.9 28.6 + - - +
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Residues in contact with GLN1033 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004D THR* 5.7 1.1 - - + -
1031D ASN* 3.1 9.2 + - - +
1032D PRO* 1.3 78.5 - - + +
1034D GLN* 1.3 62.0 + - + +
1036D ARG* 3.2 30.1 + - - +
1037D GLN* 2.9 40.2 + - - +
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Residues in contact with GLN1034 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877C PRO 3.8 6.5 - - - +
878C SER* 3.2 41.8 + - - -
880C MET* 3.9 22.3 - - + +
1030D GLY* 3.5 17.0 - - - -
1031D ASN* 2.9 37.4 + - - +
1033D GLN* 1.3 72.5 - - + +
1035D ILE* 1.3 67.6 + - + +
1037D GLN* 2.9 25.5 + - - +
1038D LEU* 2.9 18.7 + - - +
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Residues in contact with ILE1035 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877C PRO* 4.7 9.9 - - + +
1007D VAL* 4.2 9.4 - - + -
1008D PHE* 4.3 12.1 - - + -
1011D PHE* 4.0 27.4 - - + -
1020D LEU* 3.7 43.1 - - + +
1021D TYR* 6.2 0.2 - - - -
1024D ALA* 4.3 14.4 - - + -
1029D ARG 5.6 0.7 - - - +
1030D GLY* 5.3 4.0 - - - -
1031D ASN 3.2 22.1 + - - +
1032D PRO 3.8 3.4 - - - +
1034D GLN* 1.3 77.0 - - + +
1036D ARG* 1.3 57.5 + - - +
1038D LEU* 3.2 10.8 + - + +
1039D CYS* 2.9 32.8 + - - +
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Residues in contact with ARG1036 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000D THR* 3.3 30.6 - - - +
1003D VAL* 4.4 9.0 - - + -
1004D THR* 3.1 37.7 - - + +
1007D VAL* 5.1 7.4 - - + -
1008D PHE* 5.9 0.2 - - - -
1032D PRO 2.9 19.7 + - - +
1033D GLN* 3.2 35.1 + - - +
1034D GLN 3.1 0.2 - - - -
1035D ILE* 1.3 78.1 - - - +
1037D GLN* 1.3 73.1 + - - +
1040D GLY* 2.8 37.7 + - - +
1041D LEU 3.3 15.3 + - - +
1042D ARG 2.7 28.7 + - - -
1043D GLY* 4.3 2.7 - - - -
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Residues in contact with GLN1037 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880C MET* 3.5 34.3 - - - +
1033D GLN* 2.9 27.6 + - - +
1034D GLN* 2.9 15.1 + - - +
1036D ARG* 1.3 101.5 - - - +
1038D LEU* 1.3 62.3 + - - +
1040D GLY 3.7 0.9 - - - +
1041D LEU 4.0 6.3 - - - -
1042D ARG* 2.8 40.8 + - - +
1060D SER* 3.6 7.8 - - - -
1061D PHE* 3.3 27.8 + - + -
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Residues in contact with LEU1038 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876C VAL* 5.8 0.7 - - + -
877C PRO* 4.1 28.3 - - + +
880C MET* 4.2 17.7 - - + -
882C LEU* 3.7 34.5 - - + -
954D ALA* 4.6 8.5 - - + -
1020D LEU* 4.2 21.5 - - + -
1034D GLN 2.9 17.0 + - - +
1035D ILE* 3.2 12.5 + - + +
1037D GLN* 1.3 76.1 - - - +
1039D CYS* 1.3 64.4 + - - +
1060D SER* 3.2 22.2 + - - -
1061D PHE* 3.9 20.4 - - + -
1062D ARG* 3.5 14.4 + - - +
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Residues in contact with CYS1039 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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954D ALA* 3.6 15.3 - - - -
955D VAL 3.3 41.7 - - - +
956D ILE* 3.5 32.7 - - - +
1007D VAL* 4.0 14.1 - - + -
1011D PHE* 3.8 21.5 - - - -
1020D LEU* 3.9 9.2 - - - -
1035D ILE* 2.9 20.6 + - - +
1038D LEU* 1.3 75.5 - - - +
1040D GLY* 1.3 61.9 + - - +
1060D SER* 4.0 2.8 - - - -
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Residues in contact with GLY1040 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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957D PRO* 5.1 1.1 - - - -
960D LYS* 3.7 16.5 + - - -
1003D VAL* 4.8 7.6 - - - -
1007D VAL* 4.1 13.7 - - - +
1036D ARG* 2.8 22.9 + - - +
1037D GLN 3.7 0.5 - - - +
1039D CYS* 1.3 74.0 - - - +
1041D LEU* 1.3 60.0 + - - -
1060D SER* 3.0 26.9 - - - -
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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