Contacts of the helix formed by residues 1079 - 1089 (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 SER1079 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1001I SER* 4.4 2.0 - - - -
1047I ASN 4.9 0.2 + - - -
1048I HIS* 4.0 4.0 - - - +
1049I PRO* 3.2 29.8 - - - +
1050I TYR* 5.6 9.5 + - - -
1077I ARG 2.6 15.3 + - - +
1078I ALA* 1.3 74.4 - - - +
1080I GLY* 1.3 71.1 + - - +
1081I LYS 3.9 0.2 - - - -
1082I PHE* 3.2 33.5 + - - -
1083I GLU* 2.8 20.9 + - - +
1112I MET* 5.9 0.2 - - - -
1115I TYR* 4.0 13.2 + - - -
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Residues in contact with GLY1080 (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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999I ASP 5.8 0.7 - - - -
1000I MET* 5.1 10.6 - - - +
1001I SER* 4.1 19.5 + - - -
1004I GLN* 4.9 3.6 - - - +
1049I PRO* 5.1 0.4 - - - +
1078I ALA 4.0 0.4 + - - -
1079I SER* 1.3 76.2 + - - +
1081I LYS* 1.3 61.7 + - - +
1082I PHE 3.1 1.8 - - - -
1083I GLU* 3.0 23.9 + - - +
1084I LEU* 3.0 17.6 + - - +
1347I ILE* 5.4 4.9 - - - -
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Residues in contact with LYS1081 (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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998I CYS* 4.1 25.9 - - + +
999I ASP 6.1 0.2 - - - +
1000I MET* 5.0 5.4 - - - -
1046I CYS* 4.2 4.2 + - - +
1047I ASN* 2.8 59.7 + - - +
1080I GLY* 1.3 73.3 - - - +
1082I PHE* 1.3 64.9 + - + +
1084I LEU* 3.2 21.3 - - + +
1085I LEU* 2.9 27.1 + - - +
1088I ILE* 5.4 0.2 - - - +
1174I PHE* 3.6 41.0 + - + -
1204I LEU* 3.6 27.0 - - + +
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Residues in contact with PHE1082 (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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1047I ASN* 4.4 9.2 - - + -
1048I HIS* 3.4 27.6 - + + -
1077I ARG 4.8 0.4 - - - -
1079I SER* 3.2 36.8 - - - +
1080I GLY 3.1 0.4 - - - -
1081I LYS* 1.3 77.8 - - + +
1083I GLU* 1.3 59.3 + - - +
1084I LEU 3.2 1.1 - - - -
1085I LEU* 3.1 24.4 + - + +
1086I ASP* 2.8 33.5 + - - +
1108I LEU* 5.3 4.9 - - + -
1109I MET* 5.1 2.2 - - + -
1112I MET* 3.4 47.8 - - + -
1115I TYR* 3.6 24.0 - + + -
1174I PHE* 3.6 26.0 - + - -
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Residues in contact with GLU1083 (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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1074I ASP* 3.6 1.0 - - - +
1077I ARG* 3.1 31.0 + - + +
1078I ALA* 3.0 27.5 - - - +
1079I SER 2.8 19.1 + - - +
1080I GLY* 3.0 7.9 + - - +
1082I PHE* 1.3 73.3 - - - +
1084I LEU* 1.3 67.0 + - + +
1086I ASP* 3.1 18.5 + - + +
1087I ARG* 3.0 26.1 + - - +
1345I SER* 3.4 37.9 + - - +
1347I ILE* 3.2 13.9 - - + +
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Residues in contact with LEU1084 (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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996I ILE* 5.5 10.5 - - + -
997I LYS 4.5 15.5 - - - +
998I CYS* 5.5 3.1 - - - -
999I ASP 6.0 2.7 - - - +
1080I GLY 3.0 14.0 + - - +
1081I LYS* 3.2 27.4 - - + +
1082I PHE 3.2 0.4 - - - -
1083I GLU* 1.3 80.3 - - + +
1085I LEU* 1.3 56.4 + - - +
1087I ARG* 3.0 49.6 + - - +
1088I ILE* 2.9 36.6 + - + +
1204I LEU* 5.4 11.0 - - + -
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Residues in contact with LEU1085 (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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1081I LYS 2.9 16.4 + - - +
1082I PHE* 3.1 37.2 + - + +
1084I LEU* 1.3 76.1 - - - +
1086I ASP* 1.3 57.3 + - - +
1088I ILE* 2.9 31.2 + - + -
1089I LEU* 2.9 33.6 + - + +
1101I LEU* 5.4 8.1 - - + -
1112I MET* 5.3 6.7 - - + -
1115I TYR* 6.6 0.4 - - + -
1172I ILE* 3.7 30.3 - - + -
1174I PHE* 4.3 18.8 - - + -
1204I LEU* 6.1 1.3 - - + -
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Residues in contact with ASP1086 (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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1077I ARG* 3.3 33.9 - - + +
1082I PHE* 2.8 25.1 + - - +
1083I GLU* 3.1 26.1 + - + +
1085I LEU* 1.3 72.2 - - - +
1087I ARG* 1.3 66.0 + - - +
1088I ILE 3.5 0.2 + - - -
1089I LEU* 5.6 0.2 - - - -
1090I PRO* 3.9 16.5 - - - +
1091I LYS* 4.4 0.9 + - - -
1115I TYR* 5.5 5.8 - - - +
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Residues in contact with ARG1087 (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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996I ILE* 5.6 7.1 - - - +
1083I GLU 3.0 12.0 + - - +
1084I LEU* 3.0 42.5 + - - +
1086I ASP* 1.3 77.6 - - - +
1088I ILE* 1.3 54.5 + - + +
1091I LYS* 2.3 34.9 + - - +
1299I ASP* 5.1 3.0 + - - -
1300I GLU* 4.7 14.5 + - - +
1301I THR* 3.7 42.0 - - + +
1308I ARG* 4.6 8.9 + - - +
1322I ASP* 5.3 4.0 - - - +
1345I SER 5.9 2.8 - - - +
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Residues in contact with ILE1088 (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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1084I LEU* 2.9 25.7 + - + +
1085I LEU* 2.9 33.1 + - + +
1087I ARG* 1.3 77.5 - - + +
1089I LEU* 1.3 77.0 + - + +
1091I LYS* 3.3 20.4 - - - +
1092I LEU* 3.3 26.2 - - + +
1099I VAL* 5.7 1.3 - - + -
1172I ILE* 5.2 6.1 - - + -
1202I LEU* 5.2 20.6 - - + -
1204I LEU* 5.7 7.2 - - + -
1308I ARG* 3.9 28.6 + - - +
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Residues in contact with LEU1089 (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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1085I LEU* 2.9 48.4 + - + +
1086I ASP* 5.6 0.2 - - - -
1088I ILE* 1.3 88.3 - - + +
1090I PRO* 1.3 63.9 - - + +
1092I LEU* 2.6 33.9 + - + +
1093I ARG* 3.0 24.4 + - + +
1097I HIS 5.5 1.8 - - - +
1098I LYS* 6.0 3.6 - - + -
1099I VAL* 3.8 37.2 - - + +
1119I ARG* 6.1 3.4 - - + -
1172I ILE* 4.8 1.1 - - + -
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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