Contacts of the helix formed by residues 1027 - 1044 (chain A) in PDB entry 1N35
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 THR1027 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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960A ARG* 3.6 21.5 - - - +
1025A ILE 4.9 0.2 - - - +
1026A ALA* 1.3 77.7 - - - +
1028A ARG* 1.3 64.0 + - - +
1029A GLU* 3.4 19.8 + - - +
1030A GLU* 2.9 37.4 + - - +
1031A LEU* 3.1 20.6 + - - +
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Residues in contact with ARG1028 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855A MET* 4.7 16.2 - - - +
1027A THR* 1.3 72.6 - - - +
1029A GLU* 1.3 67.3 + - - +
1031A LEU* 3.3 19.3 - - + +
1032A ALA* 3.1 24.4 + - - +
1295A CH1 4.4 31.7 + - - +
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Residues in contact with GLU1029 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027A THR* 3.4 16.4 - - - +
1028A ARG* 1.3 87.2 + - + +
1030A GLU* 1.3 65.7 + - + +
1031A LEU 3.0 1.3 - - - -
1032A ALA* 2.9 10.1 + - - +
1033A GLU* 2.9 32.6 + - + +
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Residues in contact with GLU1030 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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955A PRO* 4.0 11.8 - - + +
956A LYS 3.2 22.3 + - - +
957A LYS* 3.3 10.1 - - - +
958A SER 5.1 0.3 - - - +
960A ARG* 2.7 48.9 + - - +
1026A ALA* 3.2 7.4 - - - +
1027A THR* 2.9 40.0 + - - +
1029A GLU* 1.3 76.6 - - + +
1031A LEU* 1.3 56.5 + - - +
1033A GLU* 3.4 22.4 + - - +
1034A MET* 3.1 25.5 + - - +
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Residues in contact with LEU1031 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813A PRO* 3.9 28.9 - - + -
955A PRO* 3.7 21.3 - - + +
1027A THR 3.1 12.9 + - - +
1028A ARG* 3.3 25.4 - - + +
1029A GLU 3.0 0.4 - - - -
1030A GLU* 1.3 75.3 - - - +
1032A ALA* 1.3 67.1 + - - +
1034A MET* 3.0 42.4 + - + +
1035A ASP* 3.0 12.6 + - - -
1295A CH1 4.1 32.5 - - + +
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Residues in contact with ALA1032 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855A MET 4.8 5.4 - - - +
856A ILE* 4.3 22.9 - - + +
1028A ARG 3.1 12.5 + - - +
1029A GLU* 2.9 12.2 + - - +
1031A LEU* 1.3 75.0 - - - +
1033A GLU* 1.3 65.4 + - + +
1035A ASP* 2.9 11.7 + - - +
1036A GLU* 2.8 25.8 + - - +
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Residues in contact with GLU1033 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029A GLU* 2.9 21.4 + - + +
1030A GLU* 3.5 31.4 + - - +
1031A LEU 3.2 0.2 - - - -
1032A ALA* 1.3 77.2 - - + +
1034A MET* 1.3 62.0 + - - +
1036A GLU* 3.4 7.9 + - - +
1037A THR* 3.0 27.4 + - - -
1040A ARG* 4.9 0.9 + - - -
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Residues in contact with MET1034 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813A PRO* 5.5 0.2 - - + -
815A PRO* 3.2 25.8 - - + -
952A PRO* 3.8 16.8 - - + +
953A ARG 3.7 5.4 - - - -
954A ASN* 3.4 41.3 - - - +
955A PRO* 3.6 11.4 - - + -
956A LYS* 5.4 0.9 - - + +
1030A GLU 3.1 12.8 + - - +
1031A LEU* 3.0 28.7 + - + +
1033A GLU* 1.3 76.4 - - - +
1035A ASP* 1.3 86.7 + - - +
1037A THR* 3.4 8.9 + - - -
1038A LEU* 3.3 25.2 + - + +
1295A CH1 3.9 0.9 - - - +
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Residues in contact with ASP1035 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815A PRO* 4.6 0.3 - - - +
854A THR* 3.8 9.5 - - + +
855A MET 5.7 0.3 - - - +
856A ILE* 5.5 4.8 - - + +
863A LEU* 3.0 29.4 - - + +
1031A LEU 3.0 15.8 + - - +
1032A ALA* 2.9 11.4 + - - +
1034A MET* 1.3 87.1 - - - +
1036A GLU* 1.3 55.8 + - - +
1038A LEU* 3.0 7.1 + - - +
1039A MET* 2.8 41.2 + - + +
1295A CH1 2.8 47.4 + - - +
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Residues in contact with GLU1036 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856A ILE* 4.5 20.8 - - + +
1032A ALA 2.8 20.3 + - - +
1033A GLU* 3.7 9.0 - - - +
1035A ASP* 1.3 71.9 - - - +
1037A THR* 1.3 52.8 + - - +
1039A MET* 3.2 13.0 + - - +
1040A ARG* 2.7 54.3 + - - +
1043A ARG* 3.5 32.7 + - - -
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Residues in contact with THR1037 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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951A LEU* 4.1 27.1 - - + -
952A PRO* 5.3 5.6 - - + -
1033A GLU 3.0 15.6 + - - -
1034A MET* 3.4 12.9 - - - -
1035A ASP 3.1 0.4 - - - -
1036A GLU* 1.3 77.1 - - - +
1038A LEU* 1.3 62.2 + - + +
1040A ARG* 3.3 21.5 + - - +
1041A ALA* 3.1 22.3 + - - +
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Residues in contact with LEU1038 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814A TRP* 4.8 0.4 - - + -
815A PRO* 4.8 11.0 - - + -
863A LEU* 4.0 26.0 - - + +
865A TYR* 3.2 40.8 - - + +
948A MET* 3.7 32.1 - - + +
951A LEU* 3.8 24.0 - - + +
952A PRO 4.5 11.0 - - - +
1034A MET* 3.3 17.4 + - + +
1035A ASP* 3.0 9.0 + - - +
1037A THR* 1.3 79.8 - - - +
1039A MET* 1.3 61.8 + - - +
1041A ALA* 3.5 4.0 + - - +
1042A ARG* 3.2 21.3 + - - +
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Residues in contact with MET1039 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854A THR* 3.8 21.5 - - + +
856A ILE* 5.9 6.5 - - + -
861A GLY* 5.8 2.5 - - - -
862A TYR 4.7 13.0 - - - +
863A LEU* 3.4 37.2 - - + +
1035A ASP* 2.8 19.2 + - + +
1036A GLU* 3.6 15.3 - - - +
1038A LEU* 1.3 77.1 - - - +
1040A ARG* 1.3 62.1 + - - +
1042A ARG* 3.5 12.0 + - + +
1043A ARG* 3.2 43.6 + - + +
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Residues in contact with ARG1040 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033A GLU 4.9 0.8 + - - -
1036A GLU* 2.7 38.7 + - - +
1037A THR* 3.6 29.3 + - - +
1039A MET* 1.3 71.1 - - - +
1041A ALA* 1.3 66.8 + - - +
1043A ARG* 3.1 28.5 + - - +
1044A HIS* 3.0 27.5 + - + +
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Residues in contact with ALA1041 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944A GLN* 4.2 3.8 - - - +
947A TYR* 5.1 2.0 - - + -
948A MET* 4.0 13.9 - - + +
951A LEU* 3.5 31.6 - - + -
1037A THR 3.1 7.9 + - - +
1038A LEU 3.7 4.7 - - - +
1040A ARG* 1.3 80.2 - - - +
1042A ARG* 1.3 58.8 + - - +
1043A ARG 3.5 0.3 + - - -
1044A HIS* 3.7 3.5 + - - +
1046A TYR* 3.0 40.7 + - - +
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Residues in contact with ARG1042 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLU* 2.8 41.4 + - - -
862A TYR 5.5 4.0 - - - -
863A LEU* 6.1 2.5 - - + -
864A GLN* 2.9 43.1 + - - +
866A PRO* 4.1 9.1 - - - +
941A LYS* 3.3 41.9 + - - +
944A GLN* 3.5 7.8 - - + +
948A MET* 3.5 30.2 - - + +
1038A LEU 3.2 9.0 + - - +
1039A MET* 3.7 16.2 - - - +
1040A ARG 3.2 0.6 - - - -
1041A ALA* 1.3 77.7 - - - +
1043A ARG* 1.3 59.9 + - + +
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Residues in contact with ARG1043 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941A LYS* 5.4 1.2 + - - +
1036A GLU* 3.5 23.8 + - - -
1039A MET* 3.2 32.0 + - + +
1040A ARG* 3.1 41.3 + - - +
1042A ARG* 1.3 76.9 - - + +
1044A HIS* 1.3 68.2 + - - +
1045A SER* 3.7 2.3 + - - -
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Residues in contact with HIS1044 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944A GLN* 3.1 17.7 + - - -
1040A ARG* 3.0 17.6 + - + +
1041A ALA* 3.7 3.3 - - - +
1042A ARG 3.5 1.4 - - - +
1043A ARG* 1.3 82.2 - - - +
1045A SER* 1.3 87.6 + - - +
1046A TYR* 3.6 37.6 - + - +
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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