Contacts of the strand formed by residues 1199 - 1205 (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 VAL1199 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990I GLU 2.5 32.3 + - - +
991I LYS* 3.3 12.9 - - + -
992I VAL* 3.0 25.6 + - - -
1169I ASP* 5.8 0.2 - - - -
1171I VAL* 5.5 4.5 - - + -
1187I GLN* 5.3 4.9 - - - +
1190I ALA* 4.0 32.1 - - + +
1191I HIS* 3.8 26.9 - - + +
1195I GLN* 4.3 11.9 - - + +
1196I GLN* 5.5 0.4 - - - +
1197I ASN 4.1 2.5 - - - +
1198I GLU* 1.3 72.5 - - - +
1200I ARG* 1.3 58.4 + - - +
1201I VAL* 3.3 11.1 + - + -
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Residues in contact with ARG1200 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992I VAL* 4.4 11.9 - - - -
994I TYR* 5.1 4.5 - - + -
1097I HIS* 5.4 1.0 + - - -
1169I ASP* 3.4 30.8 + - - +
1170I THR* 4.6 8.4 - - + +
1171I VAL* 2.9 34.3 + - - +
1198I GLU* 2.8 60.1 + - - +
1199I VAL* 1.3 69.7 - - - +
1201I VAL* 1.3 66.6 + - - +
1202I LEU* 5.5 8.7 - - + +
1308I ARG* 3.3 21.9 + - + +
1309I HIS* 3.2 17.9 + - - -
1310I GLU* 3.2 32.4 + - - +
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Residues in contact with VAL1201 (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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991I LYS* 4.2 18.6 - - + -
992I VAL 2.9 28.8 + - - +
993I GLU* 4.9 7.6 - - + -
994I TYR* 3.8 15.5 + - - -
1171I VAL* 3.7 11.4 - - + -
1173I ILE* 3.7 27.6 - - + -
1186I ALA 5.6 5.2 - - - +
1187I GLN* 5.9 5.6 - - + -
1199I VAL* 4.1 13.5 - - + +
1200I ARG* 1.3 80.8 - - - +
1202I LEU* 1.3 67.6 + - - +
1203I ARG* 5.4 3.1 - - + -
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Residues in contact with LEU1202 (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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994I TYR* 3.7 17.9 - - + +
996I ILE* 5.9 4.0 - - + -
1088I ILE* 5.2 19.5 - - + -
1092I LEU* 6.1 2.9 - - + -
1170I THR* 5.7 7.6 - - + -
1171I VAL 3.0 18.1 + - - +
1172I ILE* 4.0 31.0 - - + -
1173I ILE* 2.9 30.0 + - - +
1200I ARG* 5.5 9.0 - - + -
1201I VAL* 1.3 77.2 - - - +
1203I ARG* 1.3 62.3 + - - +
1204I LEU* 4.7 14.6 - - + -
1308I ARG* 5.1 18.2 - - + +
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Residues in contact with ARG1203 (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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994I TYR 2.8 15.5 + - - +
995I VAL* 3.3 15.4 - - + +
996I ILE* 3.1 27.8 + - - +
1173I ILE* 3.7 28.7 - - + +
1174I PHE 4.9 1.1 + - - -
1175I ASP* 3.1 28.5 + - - +
1176I SER* 3.2 25.3 - - - +
1182I GLN* 4.9 1.8 + - - -
1183I ASP* 4.6 12.2 + - - -
1201I VAL* 5.4 3.4 - - + -
1202I LEU* 1.3 77.4 - - - +
1204I LEU* 1.3 95.2 + - - +
1205I CYS* 3.5 14.8 - - - +
1206I THR 4.7 3.2 + - - +
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Residues in contact with LEU1204 (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* 3.4 28.5 - - + +
997I LYS 5.5 1.3 - - - +
998I CYS* 3.5 12.6 - - - -
1081I LYS* 3.6 31.6 - - + +
1084I LEU* 5.4 9.6 - - + -
1085I LEU* 6.1 1.3 - - + -
1088I ILE* 5.7 7.4 - - + -
1172I ILE* 5.8 0.2 - - + -
1173I ILE 3.4 14.2 + - - +
1174I PHE* 3.5 44.1 - - + +
1202I LEU* 4.7 13.7 - - + -
1203I ARG* 1.3 110.2 + - - +
1205I CYS* 1.3 55.6 + - - +
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Residues in contact with CYS1205 (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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995I VAL* 3.6 24.2 - - + -
996I ILE 3.3 26.0 - - - -
997I LYS* 3.7 12.6 - - - +
998I CYS* 2.9 36.4 + - - +
1174I PHE 5.7 0.4 - - - -
1203I ARG* 3.5 8.7 - - - +
1204I LEU* 1.3 76.2 - - - +
1206I THR* 1.3 66.2 + - - +
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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