Contacts of the helix formed by residues 95 - 102 (chain D) in PDB entry 6KW5
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 HIS 95 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88D TRP* 3.2 52.4 + + + -
89D PHE* 5.0 1.0 - - - -
90D ASP* 4.7 16.6 - - + -
93D LYS 5.1 0.2 - - - -
94D ILE* 1.3 84.9 - - - +
96D GLU* 1.3 81.1 + - + +
97D ILE* 3.3 24.6 + - + +
98D GLU* 3.4 11.6 + - + +
99D LYS* 3.1 22.3 + - - +
414F VAL* 5.5 7.9 - - + +
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Residues in contact with GLU 96 (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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95D HIS* 1.3 81.3 + - + +
97D ILE* 1.3 60.8 + - + +
99D LYS* 3.5 34.8 + - - +
100D ARG* 2.9 36.1 + - - +
412F ASP* 3.5 25.4 - - + +
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Residues in contact with ILE 97 (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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88D TRP* 3.7 28.9 - - + -
95D HIS* 3.3 26.5 + - + +
96D GLU* 1.3 77.8 - - + +
98D GLU* 1.3 59.0 + - - +
100D ARG* 3.5 4.9 - - - +
101D SER* 2.9 32.7 + - - -
159D PHE* 4.6 5.8 - - + -
163D TRP* 4.1 21.1 - - + -
409F ILE* 3.9 19.7 - - + +
410F TYR* 4.1 15.7 - - + -
412F ASP* 3.6 24.9 - - - +
413F VAL* 5.2 12.6 - - + +
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Residues in contact with GLU 98 (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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88D TRP* 5.0 7.5 - - + -
89D PHE* 3.8 14.2 - - - -
94D ILE* 3.3 13.6 - - + +
95D HIS* 3.4 13.9 + - - +
97D ILE* 1.3 78.6 - - + +
99D LYS* 1.3 60.0 + - - +
101D SER* 4.1 0.4 - - - -
102D ASN* 2.9 24.5 + - - +
106D PHE* 3.7 11.0 - - + -
118D TYR* 2.6 38.5 + - + +
122D ARG* 3.2 36.2 + - - -
159D PHE* 3.6 32.1 - - + -
160D LEU* 5.1 1.8 - - - +
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Residues in contact with LYS 99 (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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94D ILE* 5.3 3.4 - - + -
95D HIS 3.1 17.4 + - - +
96D GLU* 3.5 35.1 + - - +
97D ILE 3.2 0.2 - - - -
98D GLU* 1.3 79.4 - - - +
100D ARG* 1.3 59.6 + - + +
103D PRO* 3.4 27.0 - - - +
106D PHE* 3.9 34.5 - - + +
107D ASN* 5.3 11.4 - - - +
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Residues in contact with ARG 100 (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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96D GLU* 2.9 21.2 + - - +
97D ILE* 3.5 8.1 - - - +
99D LYS* 1.3 81.3 - - + +
101D SER* 1.3 68.6 + - - +
103D PRO* 4.1 9.6 - - - +
408F GLU* 2.8 37.5 + - - +
409F ILE* 3.2 55.1 + - + +
411F GLU* 6.0 0.2 - - - +
412F ASP* 3.8 24.5 + - - +
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Residues in contact with SER 101 (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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97D ILE* 2.9 18.9 + - - -
99D LYS 3.6 0.2 - - - -
100D ARG* 1.3 82.2 - - - +
102D ASN* 1.3 62.0 + - - +
103D PRO* 3.4 6.2 - - - +
159D PHE* 3.4 35.1 - - - -
162D LYS* 5.8 1.9 + - - -
163D TRP* 5.3 0.8 + - - -
409F ILE* 5.3 10.8 - - - -
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Residues in contact with ASN 102 (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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98D GLU* 2.9 28.7 - - - +
99D LYS 4.4 0.2 - - - -
101D SER* 1.3 79.6 - - - +
103D PRO* 1.3 60.2 - - - +
104D ASP 3.2 10.0 + - - -
105D PHE* 4.0 29.2 + - + -
106D PHE* 4.1 4.2 - - - -
118D TYR* 4.3 15.5 + - - -
155D LYS* 4.0 31.7 + - + +
156D ILE* 4.4 8.1 - - - +
159D PHE* 4.6 20.1 - - - +
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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