Contacts of the helix formed by residues 1001 - 1013 (chain I) in PDB entry 6LTJ
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 SER1001 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1000I MET* 1.3 79.9 - - - +
1002I ALA* 1.3 66.3 + - - +
1003I LEU* 3.2 6.5 - - - -
1004I GLN* 3.1 36.9 + - - +
1005I ARG* 3.2 8.5 + - - +
1078I ALA 3.2 23.7 + - - -
1079I SER* 4.4 0.5 - - - -
1080I GLY* 4.1 9.0 + - - -
1347I ILE* 3.3 32.0 - - - +
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Residues in contact with ALA1002 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000I MET 3.7 1.0 + - - -
1001I SER* 1.3 71.9 - - - +
1003I LEU* 1.3 58.0 + - - +
1005I ARG* 3.2 24.5 + - + +
1006I VAL* 2.9 31.6 + - + +
1009I ARG* 6.1 0.2 - - - +
1347I ILE 3.2 8.9 + - - -
1348I ILE* 3.8 26.7 - - + +
1349I LYS* 3.8 23.1 - - - +
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Residues in contact with LEU1003 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001I SER* 4.7 4.3 - - - -
1002I ALA* 1.3 78.1 - - - +
1004I GLN* 1.3 84.4 + - + +
1006I VAL* 3.2 10.7 - - + +
1007I LEU* 2.9 38.5 + - + +
1049I PRO* 5.4 1.3 - - + -
1052I PHE* 4.5 23.3 - - + -
1054I HIS* 6.0 3.1 - - - +
1055I ILE* 6.5 0.9 - - + -
1347I ILE 4.5 7.5 + - - +
1349I LYS* 5.0 5.0 - - - +
1350I ASP* 4.5 16.2 - - - +
1351I ASP* 5.1 8.1 - - - +
1355I GLU* 4.2 39.9 - - + +
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Residues in contact with GLN1004 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000I MET* 3.4 35.4 - - + +
1001I SER* 3.1 44.6 + - - +
1003I LEU* 1.3 86.7 - - + +
1005I ARG* 1.3 51.9 + - - +
1007I LEU* 3.9 10.8 - - + -
1008I TYR* 2.7 38.6 + - + +
1045I ILE* 4.5 16.7 - - + +
1049I PRO* 3.3 39.5 - - + +
1052I PHE* 5.8 1.6 - - + -
1080I GLY 4.9 2.8 - - - +
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Residues in contact with ARG1005 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999I ASP* 3.1 27.8 + - - +
1000I MET* 2.7 44.4 + - + +
1001I SER 3.2 10.1 + - - +
1002I ALA* 3.2 26.1 + - + +
1003I LEU 3.2 0.6 - - - -
1004I GLN* 1.3 77.2 - - - +
1006I VAL* 1.3 59.6 + - - +
1008I TYR* 3.1 13.0 - - + +
1009I ARG* 3.0 41.1 + - - +
1347I ILE* 5.1 5.5 - - - +
1348I ILE* 5.0 8.3 - - - +
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Residues in contact with VAL1006 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002I ALA* 2.9 18.9 + - + +
1003I LEU* 3.2 19.5 - - + +
1005I ARG* 1.3 74.0 - - - +
1007I LEU* 1.3 77.2 + - + +
1009I ARG* 3.1 39.4 + - - +
1010I HIS* 3.0 21.3 + - - +
1349I LYS* 4.0 23.8 - - + +
1355I GLU* 5.7 5.4 - - + +
1356I ARG* 6.5 0.4 - - + -
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Residues in contact with LEU1007 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003I LEU* 2.9 33.1 + - + +
1004I GLN* 3.9 9.6 - - + -
1006I VAL* 1.3 81.4 - - + +
1008I TYR* 1.3 55.0 + - - +
1010I HIS* 2.9 16.4 + - + +
1011I MET* 2.5 38.4 + - + +
1045I ILE* 6.3 2.0 - - + -
1052I PHE* 5.1 14.1 - - + -
1355I GLU* 5.2 7.0 - - + +
1356I ARG* 6.4 1.3 - - + -
1358I THR* 5.7 2.7 - - - +
1359I CYS* 3.5 40.6 - - + -
1362I GLU* 4.2 13.2 - - - +
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Residues in contact with TYR1008 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000I MET* 5.8 6.3 - - + -
1004I GLN 2.7 24.9 + - - +
1005I ARG* 3.1 15.7 - - + +
1007I LEU* 1.3 71.2 - - - +
1009I ARG* 1.3 56.3 + - + +
1011I MET* 3.1 22.0 + - + +
1012I GLN* 2.8 60.8 + - - +
1042I LEU* 3.9 27.0 - - + +
1045I ILE* 4.2 12.7 - - + +
1046I CYS* 4.4 26.7 - - + +
1206I THR* 5.1 5.9 + - - -
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Residues in contact with ARG1009 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002I ALA* 6.1 0.4 - - - +
1005I ARG* 3.0 28.1 + - - +
1006I VAL* 3.1 50.5 + - + +
1007I LEU 3.1 0.6 - - - -
1008I TYR* 1.3 78.4 - - + +
1010I HIS* 1.3 63.7 + - + +
1012I GLN* 3.2 16.8 + - - +
1013I ALA* 3.1 18.0 + - - +
1349I LYS* 6.0 0.2 - - - +
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Residues in contact with HIS1010 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006I VAL 3.0 7.4 + - - +
1007I LEU* 2.9 35.0 + - + +
1009I ARG* 1.3 77.6 - - + +
1011I MET* 1.3 55.2 + - - +
1013I ALA* 3.0 13.6 - - + -
1014I LYS* 2.7 60.2 + - + +
1359I CYS* 3.3 27.7 - - - -
1362I GLU* 3.2 19.5 + - - -
1363I GLU* 4.7 13.7 - - + +
1366I MET 4.5 0.9 + - - -
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Residues in contact with MET1011 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007I LEU* 2.5 23.3 + - + +
1008I TYR* 3.3 24.9 - - + +
1010I HIS* 1.3 72.4 + - + +
1012I GLN* 1.3 63.3 + - - +
1014I LYS* 3.2 46.8 + - + +
1041I GLN* 5.6 4.5 - - + -
1042I LEU* 3.7 39.5 - - + -
1045I ILE* 3.7 30.1 - - + -
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Residues in contact with GLN1012 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008I TYR* 2.8 65.3 + - - +
1009I ARG* 3.2 17.4 - - - +
1011I MET* 1.3 79.1 - - - +
1013I ALA* 1.3 57.6 + - - +
1014I LYS 3.2 4.3 + - - -
1042I LEU* 3.9 23.3 - - + +
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Residues in contact with ALA1013 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009I ARG 3.1 12.4 + - - +
1010I HIS* 3.0 17.5 + - + +
1012I GLN* 1.3 76.7 - - - +
1014I LYS* 1.3 61.6 + - - +
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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