Contacts of the helix formed by residues 1063 - 1070 (chain D) in PDB entry 1KF9
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 ASN1063 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1061D PRO 3.4 2.6 + - - -
1062D SER* 1.3 82.5 + - - +
1064D LYS* 1.3 61.6 + - - +
1065D GLU* 2.9 19.2 + - - +
1066D GLU* 2.8 54.6 + - - +
1067D THR* 2.9 31.0 + - - -
1298E SER 5.3 6.5 + - - +
1301E THR 4.0 15.9 + - - +
1302E SER* 4.3 6.0 + - - -
1303E ILE* 4.5 3.4 - - + -
1369E TRP* 3.2 19.6 - - + -
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Residues in contact with LYS1064 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063D ASN* 1.3 71.3 - - - +
1065D GLU* 1.3 75.2 + - - +
1066D GLU 3.2 0.3 + - - -
1067D THR 3.2 0.3 + - - -
1068D GLN* 2.9 47.7 + - + +
1244E GLU* 2.7 39.6 + - + +
1364E ASP* 2.5 40.3 + - - +
1367E LYS* 3.6 17.7 - - - +
1369E TRP* 3.2 38.8 - - + +
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Residues in contact with GLU1065 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063D ASN* 2.9 16.2 + - - +
1064D LYS* 1.3 85.8 - - - +
1066D GLU* 1.3 62.4 + - + +
1068D GLN* 4.4 3.0 - - - +
1069D GLN* 3.5 16.3 + - - +
1298E SER* 5.7 9.4 - - - +
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Residues in contact with GLU1066 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060D THR 4.5 2.1 - - - +
1061D PRO* 3.7 18.0 - - + +
1062D SER* 2.6 39.5 + - - -
1063D ASN* 2.8 33.8 + - - +
1065D GLU* 1.3 72.2 - - + +
1067D THR* 1.3 66.4 + - - +
1069D GLN* 2.8 49.9 + - - +
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Residues in contact with THR1067 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061D PRO* 3.3 23.3 + - - +
1063D ASN 2.9 24.4 + - - -
1064D LYS* 3.8 2.2 - - - -
1066D GLU* 1.3 73.2 - - - +
1068D GLN* 1.3 63.9 + - - +
1070D LYS* 3.2 20.5 + - - +
1075D LEU* 3.8 22.0 - - + +
1175D THR* 5.1 0.4 - - + -
1176D TYR* 4.0 15.9 - - + -
1179D THR* 3.9 24.7 - - + +
1369E TRP* 3.5 22.3 - - + -
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Residues in contact with GLN1068 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064D LYS* 2.9 41.6 + - + +
1065D GLU* 4.5 2.9 - - - +
1067D THR* 1.3 73.6 - - - +
1069D GLN* 1.3 57.3 + - - +
1070D LYS 3.0 6.1 - - - +
1179D THR* 4.2 14.6 + - - +
1183D ARG* 2.8 28.9 + - - +
1364E ASP* 3.5 5.4 + - - +
1367E LYS* 2.9 63.6 - - - +
1369E TRP* 4.3 8.1 - - - +
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Residues in contact with GLN1069 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061D PRO* 5.2 0.2 - - - +
1065D GLU 3.5 10.9 + - - +
1066D GLU* 2.8 35.3 + - - +
1068D GLN* 1.3 74.6 - - - +
1070D LYS* 1.3 109.8 + - + +
1071D SER* 3.6 1.7 + - - -
1074D GLU* 4.2 2.6 - - - +
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Residues in contact with LYS1070 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059D PRO* 6.1 6.3 - - - +
1061D PRO* 4.0 25.1 - - + -
1066D GLU 3.2 2.8 + - - +
1067D THR 3.2 9.6 + - - +
1068D GLN 3.0 2.4 - - - +
1069D GLN* 1.3 114.2 + - + +
1071D SER* 1.3 55.2 + - - +
1074D GLU* 3.3 30.4 + - + +
1075D LEU* 3.7 16.6 - - + -
1078D ILE* 4.5 15.7 - - + -
1183D ARG* 2.4 27.1 + - - -
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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