Contacts of the helix formed by residues 91 - 105 (chain X) in PDB entry 1ZV4
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 ALA 91 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77X GLU* 4.1 10.1 - - - +
81X TRP* 3.9 20.2 - - + +
87X LYS 3.4 10.1 + - - +
88X MET 3.1 8.6 + - - +
90X LYS* 1.3 77.6 - - - +
92X PRO* 1.3 71.2 - - + +
93X ALA* 3.2 2.0 - - + +
94X GLY 2.9 20.8 + - - +
95X ARG* 2.9 15.0 + - - +
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Residues in contact with PRO 92 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67X TYR* 4.8 16.2 - - + -
70X SER* 3.7 31.6 - - - +
90X LYS 3.6 8.7 - - - +
91X ALA* 1.3 82.8 - - + +
93X ALA* 1.3 56.5 + - - +
95X ARG* 3.5 25.7 + - - +
96X ASN* 3.0 41.7 + - - +
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Residues in contact with ALA 93 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70X SER 3.8 20.7 + - - +
71X MET 4.1 5.2 - - - +
73X PRO* 3.8 29.8 - - + -
81X TRP* 3.9 8.1 - - + -
91X ALA* 3.2 2.1 - - + +
92X PRO* 1.3 76.9 - - - +
94X GLY* 1.3 64.6 + - - +
96X ASN* 3.9 7.1 - - - +
97X LEU* 3.2 23.9 + - - +
199X PHE* 5.3 5.1 - - + -
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Residues in contact with GLY 94 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81X TRP* 3.5 24.3 - - - -
88X MET* 3.5 28.5 - - - +
91X ALA 2.9 8.5 + - - -
93X ALA* 1.3 74.6 - - - +
95X ARG* 1.3 63.4 + - - +
97X LEU* 3.3 4.2 + - - +
98X PHE* 3.1 23.6 + - - +
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Residues in contact with ARG 95 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88X MET 3.5 0.6 + - - -
89X MET* 3.1 46.7 + - - +
90X LYS* 3.7 15.6 + - - +
91X ALA 2.9 9.6 + - - +
92X PRO* 3.7 34.9 - - - +
94X GLY* 1.3 75.0 - - - +
96X ASN* 1.3 59.3 + - - +
98X PHE* 3.4 5.7 + - - -
99X ARG* 2.8 36.1 + - - +
111X LEU* 3.5 13.8 - - + +
114X TRP* 4.1 12.0 - - - -
115X LEU* 3.5 39.0 - - + +
118X GLU* 6.0 1.6 - - - +
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Residues in contact with ASN 96 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92X PRO* 3.0 29.3 + - - +
93X ALA* 3.9 7.4 - - - +
95X ARG* 1.3 79.3 - - - +
97X LEU* 1.3 64.8 + - - +
99X ARG* 3.5 19.7 + - - +
100X GLU* 3.2 20.4 + - - +
115X LEU* 6.1 2.6 - - - +
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Residues in contact with LEU 97 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81X TRP* 4.3 10.5 - - + -
93X ALA 3.2 15.1 + - - +
94X GLY 3.6 4.0 - - - +
96X ASN* 1.3 76.5 - - - +
98X PHE* 1.3 65.2 + - - +
100X GLU* 3.2 16.5 + - + +
101X PHE 3.3 9.0 + - - -
190X PHE* 3.6 27.6 - - + -
195X ILE* 3.9 21.1 - - + +
196X TYR* 4.4 8.5 - - + -
199X PHE* 3.4 61.5 - - + -
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Residues in contact with PHE 98 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85X PHE* 3.8 26.9 - + - -
88X MET* 3.8 14.1 - - + -
89X MET* 4.1 16.8 - - - -
94X GLY 3.1 16.4 + - - +
95X ARG* 3.7 4.5 - - - +
97X LEU* 1.3 76.6 - - - +
99X ARG* 1.3 56.3 + - - +
101X PHE* 3.3 2.4 + + - +
102X LEU* 2.9 69.0 + - + +
111X LEU* 4.1 6.1 - - + -
182X MET* 4.0 12.3 - - + -
186X SER* 3.8 13.9 - - - -
187X PHE* 4.0 14.4 - + - -
190X PHE* 3.6 44.4 - + + -
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Residues in contact with ARG 99 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95X ARG 2.8 17.4 + - - +
96X ASN* 3.7 20.8 - - - +
97X LEU 3.2 0.2 - - - -
98X PHE* 1.3 75.1 - - - +
100X GLU* 1.3 63.3 + - - +
102X LEU* 3.9 3.7 - - - +
103X ARG* 3.2 36.5 + - + +
108X GLU* 2.8 35.8 + - + +
111X LEU* 3.5 17.5 - - + +
112X LEU* 3.6 28.4 - - - +
115X LEU* 4.6 12.6 - - - +
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Residues in contact with GLU 100 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96X ASN 3.2 12.7 + - - +
97X LEU* 3.2 12.1 + - + +
99X ARG* 1.3 73.2 - - - +
101X PHE* 1.3 64.4 + - - +
103X ARG* 3.2 26.9 + - - +
104X THR* 3.4 11.6 + - - +
195X ILE* 4.2 17.0 - - + +
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Residues in contact with PHE 101 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97X LEU 3.3 2.8 + - - -
98X PHE* 3.5 11.0 - + - +
100X GLU* 1.3 79.1 - - - +
102X LEU* 1.3 63.8 + - + +
104X THR* 2.5 30.8 + - - -
105X GLU* 2.9 41.4 + - + +
186X SER* 3.5 22.2 - - - -
189X ARG* 3.6 7.9 - - + -
190X PHE* 3.3 49.1 - + + -
193X SER* 3.6 30.1 - - - -
195X ILE* 3.8 17.6 - - + +
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Residues in contact with LEU 102 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98X PHE* 2.9 54.3 + - + +
99X ARG* 3.9 4.0 - - - +
100X GLU 3.3 0.2 - - - -
101X PHE* 1.3 78.8 - - + +
103X ARG* 1.3 59.4 + - - +
105X GLU* 3.1 5.1 + - - +
106X TYR 2.9 23.4 + - - -
107X SER* 3.0 38.0 + - - +
108X GLU* 3.8 12.8 - - - -
111X LEU* 3.4 39.9 - - + +
182X MET* 4.4 6.1 - - + -
186X SER* 3.6 17.5 - - - +
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Residues in contact with ARG 103 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99X ARG* 3.2 30.6 + - - +
100X GLU* 3.2 16.1 + - - +
102X LEU* 1.3 77.4 - - - +
104X THR* 1.3 57.4 + - + +
106X TYR* 3.2 28.5 + - - +
108X GLU* 3.1 43.6 + - - +
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Residues in contact with THR 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100X GLU 3.6 12.8 - - - +
101X PHE* 2.5 30.1 + - - -
103X ARG* 1.3 76.7 - - + +
105X GLU* 1.3 60.6 + - - +
106X TYR* 3.4 20.2 - - - -
195X ILE* 4.0 17.5 - - + -
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Residues in contact with GLU 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X PHE* 2.9 44.3 - - + +
102X LEU* 3.1 7.5 + - - +
104X THR* 1.3 79.9 + - - +
106X TYR* 1.3 75.8 + - - +
107X SER* 3.1 13.6 + - - +
186X SER* 3.9 10.4 + - - -
189X ARG* 3.1 37.7 + - - -
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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