Contacts of the helix formed by residues 1026 - 1037 (chain G) in PDB entry 1P3M
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 PRO1026 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1018G SER* 3.8 5.2 - - - +
1025G PHE* 1.3 92.9 - - + +
1027G VAL* 1.3 65.3 + - - +
1028G GLY 3.1 2.5 - - - +
1029G ARG* 3.0 30.6 + - + +
1030G VAL* 2.9 25.2 + - + +
1052G ALA* 4.9 0.2 - - - -
1434H TYR* 4.4 9.9 - - + -
1437H TYR* 3.2 47.8 - - + +
176J A 5.4 1.1 - - - +
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Residues in contact with VAL1027 (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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1017G ARG* 3.8 26.5 - - + +
1018G SER* 3.3 36.3 + - - +
1021G ALA* 4.6 0.2 - - + -
1023G LEU* 4.0 15.5 - - + -
1025G PHE 3.6 2.2 - - - +
1026G PRO* 1.3 71.8 - - - +
1028G GLY* 1.3 62.7 + - - +
1030G VAL* 4.5 0.9 - - - -
1031G HIS* 3.1 22.2 + - - +
1048G PRO* 3.8 2.6 - - + +
1049G VAL* 3.6 37.9 - - + +
1052G ALA* 4.0 22.9 - - + -
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Residues in contact with GLY1028 (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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1017G ARG* 3.8 18.9 + - - -
1018G SER* 4.8 1.0 + - - -
1026G PRO 3.1 1.0 - - - -
1027G VAL* 1.3 81.5 - - - +
1029G ARG* 1.3 61.7 + - - +
1031G HIS* 3.5 3.6 + - - +
1032G ARG* 3.0 20.8 + - - +
176J A 3.8 19.6 + - - -
177J G 4.3 14.8 + - - -
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Residues in contact with ARG1029 (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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1026G PRO* 3.0 27.6 + - + +
1028G GLY* 1.3 74.1 - - - +
1030G VAL* 1.3 56.2 + - - +
1032G ARG* 2.9 20.8 + - - +
1033G LEU* 2.7 54.5 + - + +
1432H GLU* 3.0 30.8 + - - +
1433H SER* 3.4 36.8 + - - +
1434H TYR* 4.2 12.6 - - + +
1437H TYR* 4.1 16.3 + - - -
121I G 3.1 23.6 + - - -
122I G 3.0 18.2 + - - -
176J A 3.4 18.4 + - - +
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Residues in contact with VAL1030 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025G PHE* 5.7 0.7 - - + -
1026G PRO* 2.9 27.0 + - + +
1027G VAL 3.9 4.5 - - - +
1029G ARG* 1.3 74.8 - - - +
1031G HIS* 1.3 57.6 + - - +
1033G LEU* 3.1 8.1 + - - +
1034G LEU* 2.8 29.0 + - + +
1048G PRO* 3.8 19.5 - - + +
1051G LEU* 3.6 22.7 - - + -
1052G ALA* 4.0 19.5 - - + -
1055G LEU* 4.4 13.9 - - + -
1434H TYR* 4.9 7.6 - - + +
1467H PHE* 3.6 22.9 - - + -
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Residues in contact with HIS1031 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017G ARG* 3.2 34.2 + - - +
1027G VAL 3.1 16.0 + - - +
1028G GLY 3.5 5.2 - - - +
1030G VAL* 1.3 78.8 - - - +
1032G ARG* 1.3 63.5 + - - +
1034G LEU* 3.1 14.2 + - - +
1035G ARG* 3.1 51.6 + - - +
1043G VAL* 3.8 18.4 + - + +
1044G GLY 3.9 3.7 + - - -
1045G ALA* 4.7 3.7 - - - -
1048G PRO* 3.3 29.0 - - + +
112I T 5.1 0.6 + - - -
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Residues in contact with ARG1032 (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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1028G GLY 3.0 13.4 + - - +
1029G ARG* 2.9 18.0 + - - +
1031G HIS* 1.3 78.1 + - - +
1033G LEU* 1.3 82.8 + - - +
1035G ARG* 3.3 8.4 - - - +
1036G LYS* 3.1 69.1 + - - +
1432H GLU* 2.7 45.8 + - - -
175J A 3.4 22.4 + - - -
176J A 3.1 37.0 + - - +
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Residues in contact with LEU1033 (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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1029G ARG* 2.7 36.2 + - + +
1030G VAL* 3.5 6.3 - - - +
1032G ARG* 1.3 100.2 - - - +
1034G LEU* 1.3 61.8 + - - +
1036G LYS* 3.7 5.1 - - + -
1037G GLY* 2.9 22.0 + - - -
1039G TYR* 3.9 3.6 - - - -
1432H GLU* 5.0 0.9 - - - +
1434H TYR* 3.1 29.6 - - + +
1464H ASN* 5.5 2.2 - - - +
1467H PHE* 3.6 23.2 - - + -
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Residues in contact with LEU1034 (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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1030G VAL 2.8 18.7 + - - +
1031G HIS 3.1 8.4 + - - +
1033G LEU* 1.3 71.9 - - - +
1035G ARG* 1.3 62.1 + - - +
1037G GLY 3.2 1.0 + - - -
1038G ASN 3.8 0.9 + - - -
1039G TYR* 2.9 35.4 + - + +
1040G ALA 5.3 0.2 + - - -
1043G VAL* 4.0 31.1 - - + +
1047G ALA* 4.2 8.3 - - + -
1048G PRO* 4.1 22.7 - - + -
1051G LEU* 3.7 20.9 - - + -
1467H PHE* 3.4 24.7 - - + -
1471H ALA* 4.2 15.0 - - + -
1486H ILE* 5.2 8.1 - - + -
1491H ILE* 4.9 6.5 - - + -
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Residues in contact with ARG1035 (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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841C GLU* 5.0 1.6 - - - +
1031G HIS* 3.1 48.1 - - - +
1032G ARG* 3.3 10.1 - - - +
1034G LEU* 1.3 71.3 - - - +
1036G LYS* 1.3 73.1 + - + +
1037G GLY 2.8 10.8 + - - -
1038G ASN* 3.0 20.1 + - - -
1040G ALA 5.1 6.8 - - - +
1041G GLU 4.8 6.3 + - - -
1043G VAL* 3.8 21.9 + - + +
112I T 3.0 41.6 + - - -
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Residues in contact with LYS1036 (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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841C GLU* 6.0 0.9 - - - -
1279D HIS* 3.3 21.0 + - - -
1032G ARG* 3.1 61.5 + - + +
1033G LEU* 3.7 6.1 - - + +
1035G ARG* 1.3 82.8 - - + +
1037G GLY* 1.3 57.5 + - - +
1038G ASN* 3.3 3.5 - - - +
175J A 4.7 12.1 + - - -
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Residues in contact with GLY1037 (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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1279D HIS* 3.9 13.5 + - - -
1033G LEU 2.9 9.9 + - - -
1034G LEU 3.2 0.2 + - - -
1035G ARG 2.8 2.4 + - - -
1036G LYS* 1.3 78.5 - - - +
1038G ASN* 1.3 73.7 + - - +
1039G TYR* 3.3 35.3 - - - -
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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