Contacts of the helix formed by residues 982 - 995 (chain A) in PDB entry 3F2B
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 TYR 982 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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879A LEU 5.0 1.1 + - - -
882A LYS* 3.4 20.3 + - - +
883A SER* 3.5 32.6 + - - -
886A ASP* 2.8 35.4 + - + -
888A TYR* 3.5 44.2 - + + -
978A PHE* 4.0 13.0 - + - -
979A SER* 2.9 9.4 + - - +
981A GLU* 1.3 74.3 - - - +
983A GLN* 1.3 67.7 + - - +
984A PRO* 3.2 4.5 - - - -
985A ARG* 2.6 51.3 + - + +
986A ALA* 3.7 23.5 + - + -
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Residues in contact with GLN 983 (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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978A PHE* 4.4 9.0 - - - -
979A SER 2.9 14.9 + - - +
980A GLY 4.1 5.5 - - - +
982A TYR* 1.3 74.9 - - - +
984A PRO* 1.3 70.8 - - + +
985A ARG 3.1 0.3 + - - -
986A ALA* 3.1 5.3 + - - +
987A HIS* 3.0 35.6 + - + +
1051A PRO 3.0 24.0 + - - -
1099A ILE* 2.7 31.7 + - + +
1100A LEU 4.1 5.2 - - - +
1101A GLY* 3.3 20.8 + - - +
9T T 3.6 27.2 + - - +
10T G 4.7 3.9 + - - -
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Residues in contact with PRO 984 (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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980A GLY 3.8 10.5 - - - +
981A GLU 3.9 7.9 - - - +
982A TYR 3.2 4.9 - - - -
983A GLN* 1.3 96.8 - - + +
985A ARG* 1.3 58.8 + - + +
987A HIS* 3.2 13.7 + - + +
988A ASN* 3.0 37.0 + - - +
1079A GLU* 5.6 4.3 - - - +
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Residues in contact with ARG 985 (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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1A PO4 2.8 42.6 + - - +
882A LYS* 5.1 2.8 - - - +
886A ASP* 3.3 23.2 + - - +
888A TYR* 4.1 15.0 + - - -
981A GLU 5.3 3.4 - - - +
982A TYR* 2.6 56.3 + - + +
984A PRO* 1.3 72.7 - - + +
986A ALA* 1.3 61.6 + - - +
988A ASN* 3.5 9.8 + - - +
989A TYR* 3.0 24.3 + - - +
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Residues in contact with ALA 986 (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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879A LEU* 3.3 26.6 - - + +
882A LYS* 5.9 0.4 - - - -
978A PHE* 3.9 21.8 - - + -
982A TYR* 3.3 24.0 + - + -
983A GLN 3.1 8.2 + - - +
985A ARG* 1.3 76.3 - - - +
987A HIS* 1.3 67.1 + - - +
989A TYR* 3.2 10.8 + - - -
990A THR* 3.5 4.0 + - - +
1099A ILE* 3.7 20.0 - - + -
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Residues in contact with HIS 987 (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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983A GLN* 3.0 37.6 + - + +
984A PRO* 3.3 15.4 - - + +
986A ALA* 1.3 75.2 - - - +
988A ASN* 1.3 59.9 + - - +
990A THR* 2.9 29.4 + - - -
991A LYS 3.9 0.2 + - - -
1001A ARG* 3.8 35.0 + - - -
1052A GLY* 3.1 21.4 + - - -
1054A ILE* 3.7 19.6 - - + +
1080A TRP* 3.4 23.5 + + + +
1099A ILE* 3.2 26.4 + - + -
10T G 5.3 0.6 + - - -
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Residues in contact with ASN 988 (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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984A PRO* 3.0 24.7 + - - +
985A ARG* 3.9 8.7 - - - +
987A HIS* 1.3 72.5 - - - +
989A TYR* 1.3 65.5 + - - +
991A LYS* 3.0 32.0 + - + +
992A VAL* 3.5 9.4 + - - +
1079A GLU* 3.7 23.5 + - - +
1080A TRP* 3.7 21.6 + - - -
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Residues in contact with TYR 989 (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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878A LYS* 3.7 30.9 + - - +
879A LEU* 3.7 20.4 - - + -
882A LYS* 3.4 44.7 - - + +
985A ARG 3.0 15.2 + - - +
986A ALA* 3.2 10.3 + - - +
988A ASN* 1.3 76.5 - - - +
990A THR* 1.3 57.7 + - - +
992A VAL* 3.2 22.7 + - + -
993A LEU* 3.0 59.5 + - + +
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Residues in contact with THR 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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875A ILE* 5.1 2.2 - - + -
879A LEU* 4.1 13.7 - - + -
986A ALA 3.7 10.1 - - - +
987A HIS* 2.9 18.7 + - - +
989A TYR* 1.3 76.1 - - - +
991A LYS* 1.3 64.0 + - - +
993A LEU* 3.8 6.5 - - - +
994A PHE* 3.1 34.1 + - - +
999A VAL* 4.0 11.6 - - - +
1054A ILE* 3.7 13.6 - - + +
1080A TRP* 3.7 13.2 - - - -
1097A LEU* 4.6 8.5 - - + -
1099A ILE* 3.8 24.7 - - + -
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Residues in contact with LYS 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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988A ASN* 3.0 21.2 + - - +
990A THR* 1.3 77.0 + - - +
992A VAL* 1.3 59.3 + - + +
995A GLY* 2.9 32.6 + - - -
996A GLU* 3.5 40.9 + - + +
999A VAL* 4.0 10.5 - - + -
1079A GLU* 3.0 28.7 + - - +
1080A TRP* 3.6 48.3 - - + +
1081A ARG* 6.4 0.2 - - - +
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Residues in contact with VAL 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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988A ASN 3.5 11.9 + - - +
989A TYR* 3.2 28.6 + - + +
991A LYS* 1.3 80.8 - - + +
993A LEU* 1.3 63.9 + - + +
995A GLY* 4.0 3.3 + - - -
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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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826A ILE* 4.5 13.1 - - - +
875A ILE* 4.2 36.1 - - + +
878A LYS* 4.0 29.4 - - + -
879A LEU* 4.8 2.0 - - + -
989A TYR* 3.0 61.6 + - + +
990A THR* 4.2 5.6 - - - +
992A VAL* 1.3 81.5 - - + +
994A PHE* 1.3 61.9 + - + +
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Residues in contact with PHE 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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824A PRO* 4.5 7.4 - - + -
826A ILE* 4.3 13.7 - - + -
871A VAL* 3.9 23.1 - - + -
872A ILE* 4.9 3.6 - - + -
875A ILE* 3.5 41.7 - - + -
990A THR* 3.1 19.0 + - - +
993A LEU* 1.3 78.1 - - + +
995A GLY* 1.3 59.4 + - - +
998A ASN* 3.2 27.6 + - + +
999A VAL* 3.6 28.3 - - + -
1056A VAL* 4.2 30.1 - - + -
1057A VAL 5.4 2.9 - - - -
1097A LEU* 4.1 12.8 - - + -
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Residues in contact with GLY 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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991A LYS 2.9 15.1 + - - +
992A VAL 4.0 3.6 + - - -
993A LEU 3.6 1.4 - - - -
994A PHE* 1.3 78.8 - - - +
996A GLU* 1.3 66.3 + - - -
997A ASP 3.2 3.4 - - - -
998A ASN* 3.0 20.8 + - - -
999A VAL* 3.9 8.7 + - - +
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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