Contacts of the strand formed by residues 1184 - 1194 (chain r) in PDB entry 6FF7
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 LEU1184 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1183r LYS* 1.3 76.9 - - - +
1185r GLU* 1.3 65.3 + - - +
1186r LEU* 5.8 2.0 - - + -
1204r ILE* 5.4 7.6 - - + -
1205r THR 3.9 8.7 - - - +
1206r PRO* 4.8 2.5 - - + -
1207r ASP* 4.3 2.5 - - - +
1270r VAL* 5.7 8.1 - - + -
1280r THR* 3.8 26.5 - - - -
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Residues in contact with GLU1185 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1183r LYS 4.3 0.2 + - - -
1184r LEU* 1.3 75.2 - - - +
1186r LEU* 1.3 63.3 + - - +
1203r THR 3.7 0.2 - - - +
1204r ILE* 3.7 1.0 - - - -
1205r THR* 2.8 44.9 + - - +
1207r ASP* 4.6 9.8 - - + +
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Residues in contact with LEU1186 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1184r LEU* 5.5 3.1 - - + -
1185r GLU* 1.3 78.3 - - - +
1187r SER* 1.3 62.3 + - - +
1202r LEU* 6.0 3.4 - - + -
1203r THR 3.3 12.1 - - - +
1204r ILE* 4.6 5.4 - - + -
1270r VAL* 6.3 3.6 - - + -
1280r THR* 6.2 3.4 - - - -
1282r LEU* 5.0 18.5 - - + +
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Residues in contact with SER1187 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1186r LEU* 1.3 75.9 - - - +
1188r VAL* 1.3 63.0 + - - +
1201r GLU 4.4 0.2 - - - -
1202r LEU* 3.4 4.3 - - - +
1203r THR* 2.7 45.5 + - - -
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Residues in contact with VAL1188 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1187r SER* 1.3 79.0 - - - +
1189r HIS* 1.3 63.1 + - - +
1190r LEU* 4.1 4.7 + - + +
1200r VAL* 5.9 4.9 - - + -
1201r GLU 3.3 10.3 - - - +
1202r LEU* 4.9 3.4 - - + -
1282r LEU* 6.2 3.6 - - + -
1284r VAL* 5.8 8.1 - - + -
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Residues in contact with HIS1189 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188r VAL* 1.3 73.6 - - - +
1190r LEU* 1.3 59.6 + - - +
1199r LYS 3.7 1.4 - - - +
1200r VAL* 3.7 1.8 - - - -
1201r GLU* 2.9 45.1 + - + +
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Residues in contact with LEU1190 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188r VAL* 4.1 5.3 + - + -
1189r HIS* 1.3 75.4 - - - +
1191r GLN* 1.3 62.4 + - - +
1198r LEU* 5.9 4.3 - - + -
1199r LYS 3.3 8.1 - - - +
1200r VAL* 4.7 4.3 - - + +
1284r VAL* 6.2 4.3 - - + -
1769r ASN* 4.7 4.5 - - - +
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Residues in contact with GLN1191 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1189r HIS 4.3 0.4 + - - -
1190r LEU* 1.3 75.8 - - - +
1192r PRO* 1.3 65.2 - - - +
1193r ILE 3.6 0.3 + - - -
1198r LEU* 4.6 2.7 - - - -
1199r LYS* 2.9 38.3 + - + +
1769r ASN* 4.3 5.8 - - - +
1770r TYR* 4.1 26.7 - - + +
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Residues in contact with PRO1192 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1191r GLN* 1.3 74.5 - - - +
1193r ILE* 1.3 61.0 + - - +
1194r THR 4.9 4.9 - - - +
1197r THR 4.1 5.8 - - - +
1198r LEU* 4.2 7.2 - - + -
1289r LEU* 6.6 0.4 - - + -
1290r ILE 4.4 17.0 - - - +
1291r LEU* 4.9 9.4 - - + -
1292r PRO* 5.1 5.8 - - + -
1767r ASN* 5.2 7.7 - - + +
1769r ASN* 5.0 12.7 - - + -
1770r TYR* 4.3 16.7 - - - +
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Residues in contact with ILE1193 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1191r GLN 3.6 3.6 + - - +
1192r PRO* 1.3 75.3 - - - +
1194r THR* 1.3 61.0 + - - +
1197r THR* 2.9 22.9 + - - +
1198r LEU* 5.0 2.0 - - - -
1199r LYS* 5.1 8.3 - - + +
1292r PRO* 4.7 8.0 - - - +
1723r PRO* 4.4 15.5 - - - +
1767r ASN* 5.9 1.4 - - - +
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Residues in contact with THR1194 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192r PRO* 4.9 4.8 - - - +
1193r ILE* 1.3 81.2 + - - +
1195r ARG* 1.3 66.9 + - - +
1196r SER* 2.9 11.3 + - - -
1197r THR* 3.0 22.3 + - - +
1291r LEU* 5.6 0.3 - - - +
1292r PRO* 4.6 10.1 - - - -
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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