Contacts of the strand formed by residues 967 - 971 (chain A) in PDB entry 6FUL
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 VAL 967 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940A THR* 4.0 18.6 - - + -
941A PRO* 3.2 28.5 - - + +
965A ASN 3.2 3.3 - - - -
966A PRO* 1.3 77.7 - - - +
968A THR* 1.3 69.5 + - - +
1168A VAL* 3.7 25.8 - - + -
1208A TYR* 4.4 8.1 - - + -
1210A PHE* 3.8 20.4 - - + -
1218A VAL* 3.8 15.9 - - + -
1219A TRP* 3.3 14.8 - - - +
1220A ILE* 3.7 17.0 - - + -
1221A ASN* 4.6 0.7 - - - +
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Residues in contact with THR 968 (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 PRO* 3.4 7.6 - - - +
943A ILE* 3.7 33.7 - - + -
959A PHE* 3.7 28.9 + - + -
960A CYS* 3.8 27.1 + - - -
965A ASN* 4.2 3.3 - - - +
967A VAL* 1.3 79.7 + - - +
969A VAL* 1.3 67.9 + - - +
970A ILE* 4.0 2.8 + - + +
1217A LEU 3.8 0.5 - - - +
1218A VAL* 3.7 1.9 - - - -
1219A TRP* 2.8 38.0 + - - +
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Residues in contact with VAL 969 (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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940A THR* 3.9 12.2 - - + +
941A PRO 3.0 10.0 + - - +
942A SER* 3.5 23.1 - - - +
943A ILE 2.9 24.9 + - - +
968A THR* 1.3 73.9 - - - +
970A ILE* 1.3 62.3 + - - +
971A ARG* 3.6 46.7 + - - +
1210A PHE* 4.0 24.9 - - + -
1211A ILE 4.8 0.4 - - - +
1212A GLN* 5.1 0.7 - - - -
1216A ASP* 4.4 9.2 - - + -
1217A LEU 3.6 8.5 - - - +
1218A VAL* 4.3 6.3 - - + +
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Residues in contact with ILE 970 (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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943A ILE* 3.6 17.5 - - + -
945A LEU* 3.5 37.0 - - + -
956A LEU* 4.7 4.3 - - + -
960A CYS* 4.2 19.7 - - - -
968A THR* 4.2 14.8 - - + +
969A VAL* 1.3 72.9 - - - +
971A ARG* 1.3 62.9 + - - +
972A GLY 3.7 0.2 + - - -
973A LEU* 3.9 17.2 + - + -
1109A PHE* 4.2 17.0 - - + -
1110A VAL* 5.3 0.4 - - + -
1216A ASP* 3.5 3.6 - - - -
1217A LEU* 2.8 59.4 + - + +
1219A TRP* 5.3 0.4 - - + -
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Residues in contact with ARG 971 (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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940A THR* 5.9 0.6 - - - -
942A SER* 4.9 4.6 + - - -
943A ILE 2.7 19.3 + - - +
944A TYR* 3.9 30.2 - - + -
945A LEU* 3.0 28.5 + - - +
969A VAL* 3.6 36.3 - - + +
970A ILE* 1.3 71.7 - - - +
972A GLY* 1.3 64.9 + - - +
973A LEU 3.4 0.7 + - - -
1210A PHE* 4.4 11.3 - - - +
1211A ILE* 2.7 30.1 + - - +
1213A ARG* 3.7 26.1 - - - +
1216A ASP* 2.8 34.8 + - - -
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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