Contacts of the helix formed by residues 989 - 997 (chain A) 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 ASP 989 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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799A PRO* 6.4 1.6 - - + -
801A ILE* 6.2 4.7 - - + -
987A LYS 4.1 2.2 + - - -
988A ILE* 1.3 70.7 - - - +
990A LEU* 1.3 60.3 + - - +
991A THR* 3.2 5.8 + - - +
992A LEU* 3.5 13.8 + - + +
993A LEU* 2.9 27.4 + - - +
1028A TYR* 4.6 6.3 - - - +
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Residues in contact with LEU 990 (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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988A ILE 3.5 4.6 + - - +
989A ASP* 1.3 71.3 - - - +
991A THR* 1.3 59.9 + - - +
993A LEU* 3.7 9.8 - - - +
994A ASN* 2.9 29.8 + - - +
1010A THR* 4.3 21.0 - - - +
1013A ASN* 5.8 6.3 - - + -
1027A SER 4.9 13.0 + - - +
1028A TYR* 4.8 3.1 + - - +
80L THR* 6.1 2.4 - - - -
81L GLN* 6.3 3.4 - - + -
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Residues in contact with THR 991 (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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989A ASP* 3.2 4.1 - - - +
990A LEU* 1.3 76.3 - - - +
992A LEU* 1.3 61.2 + - - +
994A ASN* 3.3 6.3 + - - +
995A ARG* 3.0 28.2 + - - +
288C ALA* 6.6 0.2 - - - -
77L LEU 4.4 16.6 - - - -
78L MET* 5.1 11.0 - - - +
79L PRO 5.8 2.0 - - - -
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Residues in contact with LEU 992 (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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806A ALA* 5.0 16.4 - - + -
989A ASP* 3.5 16.7 + - + +
991A THR* 1.3 77.0 - - - +
993A LEU* 1.3 56.8 + - - +
995A ARG* 3.4 7.5 + - - +
996A LEU* 2.9 30.0 + - - +
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Residues in contact with LEU 993 (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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988A ILE* 5.5 7.2 - - + -
989A ASP 2.9 19.7 + - - +
990A LEU* 3.7 9.6 - - - +
991A THR 3.2 0.2 - - - -
992A LEU* 1.3 77.0 - - - +
994A ASN* 1.3 57.6 + - - +
996A LEU* 3.2 5.6 + - - +
997A LEU* 2.9 32.2 + - - +
1010A THR* 5.4 4.5 - - - -
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Residues in contact with ASN 994 (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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990A LEU 2.9 19.0 + - - +
991A THR* 3.7 6.1 - - - +
993A LEU* 1.3 76.1 - - - +
995A ARG* 1.3 62.0 + - - +
997A LEU* 4.1 1.3 - - - +
998A ARG* 3.3 26.9 + - - +
1006A ALA* 4.9 9.8 - - - +
1007A ASP* 5.8 2.7 - - - -
1010A THR* 4.0 20.1 - - - -
79L PRO* 5.8 7.4 - - + -
80L THR* 5.8 4.5 - - - +
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Residues in contact with ARG 995 (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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810A TYR* 6.2 1.1 - - - +
991A THR 3.0 16.7 + - - +
992A LEU* 3.9 7.0 - - - +
994A ASN* 1.3 76.7 - - - +
996A LEU* 1.3 61.8 + - - +
998A ARG* 4.3 5.4 + - - +
999A LEU* 4.6 5.7 + - - +
291C LEU* 5.1 15.5 - - + -
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Residues in contact with LEU 996 (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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810A TYR* 6.5 1.1 - - - -
813A THR* 5.9 7.6 - - - -
992A LEU 2.9 18.1 + - - +
993A LEU* 3.7 6.1 - - - +
995A ARG* 1.3 74.8 - - - +
997A LEU* 1.3 59.3 + - + +
998A ARG 3.2 4.7 - - - -
999A LEU* 3.2 27.4 + - - +
1000A ILE* 4.4 0.9 + - - +
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Residues in contact with LEU 997 (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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993A LEU 2.9 16.7 + - - +
994A ASN* 4.1 1.8 - - - -
996A LEU* 1.3 74.7 - - + +
998A ARG* 1.3 57.5 + - - +
999A LEU 3.3 0.7 - - - -
1000A ILE* 4.8 5.2 - - + +
1001A VAL* 3.3 28.5 + - + +
1006A ALA* 3.9 10.1 - - + +
1043A TYR* 6.0 6.1 - - + -
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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