Contacts of the helix formed by residues 83 - 94 (chain A) in PDB entry 4KZZ
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 GLY 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A SER* 3.4 17.0 - - - -
80A ARG* 3.3 4.6 + - - +
81A ASN 2.6 5.5 + - - -
82A THR* 1.3 79.6 + - - +
84A GLN* 1.3 55.2 + - - +
86A ALA* 3.3 13.4 - - - +
87A VAL* 3.1 34.5 + - - +
125A THR* 5.1 3.6 - - - -
171A VAL* 3.8 11.9 - - - -
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Residues in contact with GLN 84 (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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78A SER* 3.9 13.2 - - - +
79A SER 4.0 6.1 + - - +
80A ARG 3.3 9.3 + - - +
81A ASN* 2.7 49.6 + - - +
82A THR 3.6 0.2 - - - -
83A GLY* 1.3 67.1 - - - +
85A ARG* 1.3 58.9 + - - +
86A ALA 3.2 0.7 - - - -
87A VAL* 3.3 8.5 - - - +
88A LEU* 2.5 36.3 - - + +
100A ALA* 3.9 12.9 - - + +
101A GLY* 3.9 21.2 - - - +
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Residues in contact with ARG 85 (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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81A ASN 4.5 1.4 + - - -
84A GLN* 1.3 74.6 - - - +
86A ALA* 1.3 67.2 + - - +
88A LEU* 3.1 8.3 + - + +
89A LYS* 2.9 41.6 + - + +
200A ASP* 3.8 7.5 + - - +
201A LEU* 2.5 57.1 + - - +
202A TYR* 5.2 0.2 - - - -
203A PHE* 3.2 26.6 + - - +
204A TYR* 5.0 9.0 + - - +
205A ARG* 5.0 15.8 - - + +
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Residues in contact with ALA 86 (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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82A THR 4.2 6.0 + - - +
83A GLY* 3.3 25.3 - - - +
85A ARG* 1.3 80.9 - - - +
87A VAL* 1.3 62.1 + - - +
90A PHE* 3.2 3.6 + - - +
171A VAL 4.7 4.9 - - - +
172A GLY* 4.9 1.3 - - - -
175A TRP* 4.0 23.8 - - + -
202A TYR* 3.1 41.0 - - + +
203A PHE 4.6 8.9 - - - +
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Residues in contact with VAL 87 (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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76A VAL* 2.9 42.0 - - + +
77A ILE 4.0 3.4 - - - -
78A SER* 3.8 22.7 - - - +
83A GLY 3.1 14.8 + - - +
84A GLN* 3.3 16.2 - - - +
86A ALA* 1.3 72.0 - - - +
88A LEU* 1.3 76.4 + - + +
90A PHE* 3.1 4.2 + - - +
91A ALA* 2.9 25.5 + - - +
98A PRO* 5.8 3.7 - - + +
99A ILE 5.6 1.6 - - - +
100A ALA* 4.7 8.3 - - + +
175A TRP* 3.6 19.1 - - + +
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Residues in contact with LEU 88 (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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84A GLN* 2.5 33.9 - - + +
85A ARG* 3.1 12.9 + - + +
87A VAL* 1.3 88.6 - - + +
89A LYS* 1.3 66.7 + - + +
91A ALA* 3.5 5.9 + - + +
92A ALA* 3.2 20.6 + - - +
98A PRO* 4.7 19.5 - - + -
100A ALA* 4.4 16.4 - - + -
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Residues in contact with LYS 89 (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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85A ARG* 2.9 34.8 + - + +
86A ALA 3.4 5.8 - - - +
88A LEU* 1.3 80.3 - - + +
90A PHE* 1.3 64.8 + - - +
92A ALA* 3.1 19.0 + - + +
93A ALA* 3.2 11.8 + - - +
201A LEU* 3.3 51.1 - - + +
202A TYR* 3.2 40.7 + - + -
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Residues in contact with PHE 90 (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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65A ILE* 4.0 31.4 - - + -
74A VAL* 4.4 5.8 - - + -
76A VAL* 2.5 41.3 - - + -
86A ALA 3.2 7.3 + - - +
87A VAL* 3.1 8.5 + - - +
89A LYS* 1.3 77.2 - - - +
91A ALA* 1.3 60.4 + - - +
93A ALA* 3.4 0.7 + - - +
94A THR* 2.8 54.4 + - + -
96A ALA* 3.7 11.2 - - + -
175A TRP* 3.8 25.4 - + + -
178A LEU* 4.3 8.5 - - + -
179A ALA* 3.5 37.7 - - + -
182A VAL* 4.2 3.1 - - + -
202A TYR* 3.2 14.8 + - + +
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Residues in contact with ALA 91 (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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76A VAL* 5.6 1.3 - - + -
87A VAL 2.9 15.1 + - - +
88A LEU* 3.7 9.4 - - + +
90A PHE* 1.3 77.7 - - + +
92A ALA* 1.3 58.7 + - - +
94A THR 2.6 18.5 - - - +
95A GLY 2.8 9.9 - - - +
96A ALA* 2.9 31.0 - - + +
97A THR 4.6 8.1 - - - -
98A PRO* 4.7 11.7 - - + -
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Residues in contact with ALA 92 (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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88A LEU 3.2 13.3 + - - +
89A LYS* 3.1 18.9 + - + +
91A ALA* 1.3 78.3 - - - +
93A ALA* 1.3 62.5 + - + +
94A THR 3.8 0.9 - - - +
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Residues in contact with ALA 93 (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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89A LYS 3.2 11.5 + - - +
90A PHE 4.1 2.2 - - - +
92A ALA* 1.3 80.5 - - - +
94A THR* 1.3 68.7 + - + +
179A ALA* 4.7 3.1 - - + -
183A LEU* 4.1 31.3 - - + +
195A TRP* 6.0 2.5 - - + -
202A TYR* 4.5 8.3 - - - +
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Residues in contact with THR 94 (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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65A ILE* 5.6 4.0 - - - -
71A PRO* 5.6 1.1 - - - -
90A PHE* 2.8 43.8 + - + +
91A ALA 2.6 28.9 - - - +
92A ALA 3.7 1.2 - - - +
93A ALA* 1.3 83.1 - - - +
95A GLY* 1.3 55.1 + - - +
96A ALA* 3.5 3.3 - - - +
179A ALA* 4.3 3.8 - - + +
182A VAL* 2.8 40.2 - - + -
183A LEU* 3.9 16.6 - - + -
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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