Contacts of the helix formed by residues 90 - 102 (chain A) in PDB entry 3ZG6
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 THR 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ILE 3.3 21.6 + - - +
54A SER* 4.4 0.7 - - - -
56A ALA* 4.1 9.9 - - + -
57A SER* 3.8 33.9 - - - +
89A PRO* 1.3 78.2 - - - +
91A GLN* 1.3 67.0 + - - +
92A THR* 3.3 5.2 + - - +
93A HIS* 2.9 31.3 + - + +
94A MET* 3.0 21.5 + - - +
257A ASP* 3.7 15.0 + - - +
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Residues in contact with GLN 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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89A PRO 5.4 0.6 + - - -
90A THR* 1.3 78.0 + - - +
92A THR* 1.3 57.7 + - - +
94A MET* 3.4 8.9 + - - +
95A ALA* 2.8 31.2 + - - +
257A ASP* 3.8 18.8 + - + +
260A MET* 5.4 0.9 - - - -
261A THR* 4.6 10.9 + - - +
271A ILE* 3.8 45.2 + - + +
272A PRO 4.7 2.8 + - - -
273A ALA* 6.1 1.0 - - - +
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Residues in contact with THR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 3.8 25.3 - - + +
90A THR* 3.2 3.7 - - - +
91A GLN* 1.3 73.2 - - - +
93A HIS* 1.3 65.1 + - - +
95A ALA* 3.2 5.6 + - - +
96A LEU* 3.2 27.3 + - - +
211A LEU* 4.2 9.9 - - - +
256A VAL* 3.5 20.6 - - + +
257A ASP* 2.6 47.6 + - - +
260A MET* 3.6 17.7 - - + -
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Residues in contact with HIS 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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53A ILE* 3.3 35.9 + - + -
54A SER* 3.3 16.2 + - - -
89A PRO* 3.7 18.8 - - + -
90A THR* 2.9 52.1 + - + +
92A THR* 1.3 77.7 + - - +
94A MET* 1.3 62.9 + - - +
96A LEU* 3.4 10.6 + - - +
97A VAL* 3.3 21.9 + - - +
112A ASN* 5.0 1.1 - - - -
114A ASP* 4.7 2.7 - - - -
116A LEU* 3.6 28.7 - - + +
117A HIS* 3.5 27.2 + + + -
120A SER* 4.4 7.0 + - - +
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Residues in contact with MET 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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89A PRO* 3.7 26.2 - - + +
90A THR 3.0 18.1 + - - +
91A GLN* 4.5 6.3 - - - +
93A HIS* 1.3 72.4 - - - +
95A ALA* 1.3 65.5 + - - +
97A VAL* 3.3 10.8 + - + +
98A GLN 3.2 15.8 + - - -
120A SER* 3.7 28.5 - - - +
271A ILE* 3.5 12.8 - - + -
272A PRO* 3.5 41.1 - - + +
273A ALA 4.1 6.3 - - - +
274A TRP* 3.9 34.3 - - + +
278A ARG* 4.0 13.5 - - - +
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Residues in contact with ALA 95 (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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91A GLN 2.8 21.6 + - - +
92A THR 3.2 5.5 + - - +
94A MET* 1.3 73.7 - - - +
96A LEU* 1.3 57.9 + - - +
98A GLN* 3.1 4.6 + - - +
99A LEU* 2.9 32.3 + - - +
260A MET* 4.2 21.8 - - + -
264A MET* 3.7 32.9 - - + +
271A ILE* 3.9 9.6 - - + +
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Residues in contact with LEU 96 (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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47A PHE* 3.5 43.1 - - + -
49A THR* 4.0 19.3 - - + -
53A ILE* 4.6 0.9 - - + -
92A THR* 3.2 24.5 + - - +
93A HIS* 3.6 6.5 - - - +
95A ALA* 1.3 72.2 - - - +
97A VAL* 1.3 66.7 + - - +
99A LEU* 3.8 5.0 - - + +
100A GLU* 3.2 23.9 + - - +
105A LEU* 3.7 16.5 - - + +
108A LEU* 4.3 5.4 - - + -
117A HIS* 3.8 24.9 - - + +
122A PHE* 3.7 14.0 - - + -
211A LEU* 4.4 2.5 - - + -
260A MET* 4.0 9.6 - - + -
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Residues in contact with VAL 97 (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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93A HIS 3.3 9.8 + - - +
94A MET* 3.3 13.4 + - + +
95A ALA 3.3 0.4 - - - -
96A LEU* 1.3 76.9 - - - +
98A GLN* 1.3 64.1 + - - +
100A GLU* 3.4 3.6 + - - +
101A ARG* 3.1 40.3 + - + +
117A HIS* 6.6 0.2 - - + -
120A SER* 3.6 34.8 - - - +
121A GLY 4.7 8.3 - - - +
122A PHE* 4.0 23.1 - - + +
123A PRO* 5.8 2.5 - - + -
272A PRO* 5.1 8.3 - - + -
278A ARG* 4.3 19.7 - - - +
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Residues in contact with GLN 98 (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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94A MET 3.2 2.2 + - - +
95A ALA 3.1 8.9 + - - +
97A VAL* 1.3 79.5 - - - +
99A LEU* 1.3 65.6 + - - +
101A ARG* 3.1 25.6 + - - +
102A VAL* 3.1 34.0 + - + +
264A MET* 3.8 13.9 - - + -
269A LEU* 4.6 10.1 - - + +
270A GLU 3.6 16.4 + - - +
272A PRO* 3.2 36.1 - - + +
287A LEU* 4.6 10.3 - - - +
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Residues in contact with LEU 99 (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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39A VAL* 5.3 2.2 - - + -
47A PHE* 3.7 32.3 - - + -
95A ALA 2.9 18.8 + - - +
96A LEU* 3.8 8.1 - - + +
97A VAL 3.4 0.2 - - - -
98A GLN* 1.3 76.0 - - - +
100A GLU* 1.3 58.7 + - - +
102A VAL* 3.3 4.6 + - - +
103A GLY 3.2 4.0 + - - -
104A LEU* 2.8 45.1 + - + +
105A LEU* 3.9 14.4 - - + -
260A MET* 3.9 18.4 - - + -
263A LEU* 4.6 6.1 - - + -
264A MET* 3.6 24.7 - - - -
267A LEU* 3.8 19.7 - - + -
269A LEU* 3.9 9.6 - - + -
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Residues in contact with GLU 100 (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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96A LEU 3.2 17.3 + - - +
97A VAL 3.8 3.5 - - - +
98A GLN 3.1 0.6 - - - -
99A LEU* 1.3 73.6 - - - +
101A ARG* 1.3 80.7 + - - +
102A VAL 3.1 1.2 + - - -
103A GLY* 3.2 11.3 + - - -
105A LEU* 3.9 32.2 - - + +
122A PHE* 3.9 13.5 - - + -
123A PRO* 3.7 30.6 - - + +
126A LYS* 2.7 32.4 + - + -
280A LEU* 6.0 0.2 - - - +
283A ALA* 3.7 9.2 - - - +
284A LEU* 4.8 4.8 + - - +
286A PRO* 4.9 4.3 - - - +
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Residues in contact with ARG 101 (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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97A VAL* 3.1 34.9 + - + +
98A GLN* 3.1 22.9 + - - +
100A GLU* 1.3 88.5 + - - +
102A VAL* 1.4 51.4 + - - +
103A GLY 3.4 0.2 - - - -
280A LEU* 5.8 3.1 - - - -
284A LEU* 3.4 38.6 + - - +
285A PRO 2.8 29.5 + - - -
286A PRO* 3.3 7.5 - - - +
287A LEU* 2.7 76.7 + - + +
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Residues in contact with VAL 102 (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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98A GLN* 3.1 31.8 + - - +
99A LEU* 3.5 13.2 - - - +
100A GLU 3.1 0.6 - - - -
101A ARG* 1.4 77.1 - - - +
103A GLY* 1.3 59.9 + - - +
104A LEU* 4.0 24.7 - - + +
269A LEU* 3.9 27.1 - - + -
286A PRO* 4.5 1.0 - - - +
287A LEU* 3.8 24.0 - - + +
288A PRO 4.2 16.6 - - - +
289A ARG* 3.8 19.2 - - - +
290A PRO* 4.7 4.0 - - + -
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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