Contacts of the helix formed by residues 73 - 85 (chain D) in PDB entry 4ZRI
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 73 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 4.1 17.9 - - + -
144B TYR* 3.7 15.9 - + - -
206B GLU* 2.5 44.9 + - - -
209B LYS* 3.3 20.5 + - + -
210B ILE* 3.6 48.0 - - + -
213B ASP* 6.1 1.1 - - - -
71D GLY 3.1 9.2 - - - +
72D PRO* 1.3 104.2 - - + +
74D GLN* 1.3 65.9 + - - +
75D LYS* 3.6 1.6 - - - -
76D ALA* 3.4 10.4 + - + +
77D LEU* 2.9 35.5 + - + +
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Residues in contact with GLN 74 (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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71D GLY* 2.8 38.2 + - - +
72D PRO 3.5 2.4 - - - -
73D TYR* 1.3 75.6 - - - +
75D LYS* 1.3 66.1 + - - +
77D LEU* 3.1 13.1 + - + +
78D ARG* 2.8 31.4 + - - +
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Residues in contact with LYS 75 (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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72D PRO 5.4 2.2 + - - +
73D TYR 3.6 0.9 - - - -
74D GLN* 1.3 76.1 - - - +
76D ALA* 1.3 58.7 + - - +
78D ARG* 3.1 28.2 + - - +
79D GLU* 2.8 43.2 + - - +
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Residues in contact with ALA 76 (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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140B LEU* 4.0 17.9 - - + -
191B TRP* 3.6 34.1 - - + -
73D TYR* 3.4 12.7 + - + +
74D GLN 3.3 0.6 - - - -
75D LYS* 1.3 75.5 - - - +
77D LEU* 1.3 67.2 + - - +
79D GLU* 3.2 2.7 + - - +
80D ILE* 2.9 31.3 + - + +
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Residues in contact with LEU 77 (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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136B GLU* 3.3 23.8 - - + +
137B ALA* 3.6 40.4 - - + +
140B LEU* 3.8 20.2 - - + -
210B ILE* 5.4 7.9 - - + -
71D GLY 6.0 1.3 - - - +
73D TYR* 2.9 37.1 + - + +
74D GLN* 3.6 10.1 - - + +
76D ALA* 1.3 71.3 - - - +
78D ARG* 1.3 56.6 + - - +
80D ILE* 4.7 1.8 - - + -
81D ARG* 3.0 36.0 + - - +
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Residues in contact with ARG 78 (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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74D GLN* 2.8 15.1 + - - +
75D LYS* 3.3 36.8 + - - +
77D LEU* 1.3 74.8 - - - +
79D GLU* 1.3 66.3 + - - +
81D ARG* 3.2 21.6 + - - +
82D TYR* 2.9 31.8 + - + +
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Residues in contact with GLU 79 (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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187B ARG* 5.2 1.2 + - - -
191B TRP* 3.1 31.0 - - + -
75D LYS* 2.8 32.6 + - - +
76D ALA* 3.7 3.7 - - - +
78D ARG* 1.3 78.4 + - + +
80D ILE* 1.3 61.9 + - - +
82D TYR* 3.5 7.9 + - - +
83D SER* 3.0 24.4 + - - -
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Residues in contact with ILE 80 (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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136B GLU* 3.7 30.5 - - + +
139B VAL* 3.6 33.9 - - + -
140B LEU* 4.0 17.0 - - + +
187B ARG* 5.7 2.7 - - - +
191B TRP* 3.5 34.5 - - + +
76D ALA 2.9 23.7 + - - +
77D LEU* 3.9 4.5 - - - +
79D GLU* 1.3 74.2 - - - +
81D ARG* 1.3 63.5 + - - +
83D SER* 3.1 9.5 + - - +
84D LEU* 2.8 41.7 + - + +
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Residues in contact with ARG 81 (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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136B GLU* 2.5 52.6 + - - +
177B TYR* 5.7 4.3 - - - +
74D GLN 5.7 0.2 + - - -
77D LEU* 3.0 30.2 + - - +
78D ARG* 3.2 39.2 + - - +
80D ILE* 1.3 75.6 - - - +
82D TYR* 1.3 62.8 + - - +
84D LEU* 3.3 7.8 + - - +
85D LEU* 3.0 33.6 + - + +
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Residues in contact with TYR 82 (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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78D ARG* 2.9 18.1 + - + +
79D GLU* 3.6 8.7 - - - +
81D ARG* 1.3 74.3 - - - +
83D SER* 1.3 66.3 + - - +
85D LEU* 3.1 35.8 + - + +
86D PRO* 3.5 5.4 - - - +
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Residues in contact with SER 83 (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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179B MET* 5.2 0.9 - - - +
187B ARG* 3.1 39.0 + - - -
79D GLU 3.0 10.7 + - - -
80D ILE* 3.1 13.3 + - - +
82D TYR* 1.3 82.9 - - - +
84D LEU* 1.3 62.1 + - - +
86D PRO* 3.4 11.3 - - - +
87D PHE* 3.7 14.9 - - - -
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Residues in contact with LEU 84 (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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135B PRO* 4.0 33.2 - - + +
136B GLU* 4.3 2.2 - - - +
139B VAL* 4.5 2.0 - - + -
177B TYR* 3.7 27.0 - - + +
179B MET* 4.1 18.6 - - + -
184B TRP* 3.8 31.6 - - + -
187B ARG* 5.1 9.9 - - + -
80D ILE* 2.8 42.1 + - + +
81D ARG* 3.5 6.7 - - - +
83D SER* 1.3 81.8 + - - +
85D LEU* 1.3 66.2 + - - +
87D PHE* 3.1 21.3 + - - -
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Residues in contact with LEU 85 (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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177B TYR* 5.1 5.6 - - + +
81D ARG* 3.0 26.3 + - + +
82D TYR* 3.1 30.2 + - + +
84D LEU* 1.3 74.8 - - - +
86D PRO* 1.4 67.0 - - + +
87D PHE 2.9 2.6 + - - -
88D ALA* 3.5 18.0 - - - +
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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