Contacts of the helix formed by residues 91 - 105 (chain M) in PDB entry 2ZHX
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 PRO 91 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70M TYR* 3.4 49.6 - - + +
75M HIS* 4.4 10.1 - - - +
83M VAL* 3.7 21.1 - - + -
87M VAL* 4.4 7.0 - - + -
89M PRO 4.3 2.0 - - - +
90M TRP* 1.3 87.4 - - + +
92M ARG* 1.3 68.8 + - - +
93M SER 3.1 1.1 - - - -
94M LEU* 2.7 19.9 + - + +
95M ALA 2.9 9.4 + - - -
19N GLN* 3.4 17.2 - - + +
20N GLU* 4.0 6.3 - - - +
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Residues in contact with ARG 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89M PRO* 5.4 1.6 - - - +
90M TRP* 2.6 40.5 + - - +
91M PRO* 1.3 70.6 - - - +
93M SER* 1.3 56.3 + - - +
95M ALA* 3.1 29.6 - - - +
96M ASN* 2.8 32.9 + - - +
194M PRO* 3.7 19.3 - - + -
19N GLN* 3.6 5.4 + - - +
20N GLU* 3.3 6.0 + - + +
45N THR* 3.9 17.0 - - + -
46N ALA 4.8 0.2 - - - -
47N TYR* 3.1 67.1 - - + +
54N ASN* 3.2 28.6 + - - +
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Residues in contact with SER 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70M TYR* 5.4 3.4 - - - -
81M PHE* 5.1 7.2 - - - -
92M ARG* 1.3 72.4 - - - +
94M LEU* 1.3 52.1 + - - +
96M ASN* 3.2 3.3 + - - +
97M ILE* 2.8 38.0 + - - +
191M HIS* 3.4 29.5 - - - -
192M PRO* 3.6 14.6 - - - +
193M SER* 3.4 10.4 - - - -
194M PRO* 4.3 1.1 - - - +
20N GLU* 2.5 39.6 + - - -
22N ILE* 4.9 1.6 - - - -
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Residues in contact with LEU 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70M TYR* 3.9 16.3 + - - +
81M PHE* 3.8 17.2 - - - +
83M VAL* 3.9 15.9 - - + -
90M TRP* 4.3 12.3 - - + -
91M PRO* 2.7 16.4 + - + +
93M SER* 1.3 71.1 - - - +
95M ALA* 1.3 65.3 + - - +
97M ILE* 3.0 23.1 + - + +
98M PHE* 2.9 51.5 + - + +
113M GLY* 3.6 29.8 - - - +
115M LEU* 4.1 13.5 - - + -
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Residues in contact with ALA 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90M TRP* 3.8 21.6 - - + +
91M PRO 2.9 4.6 + - - -
92M ARG* 3.1 42.4 - - - +
94M LEU* 1.3 77.7 - - - +
96M ASN* 1.3 65.3 + - - +
98M PHE* 3.2 6.8 + - - +
99M ASP* 2.9 26.8 + - - +
109M LEU* 5.4 0.5 - - - +
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Residues in contact with ASN 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92M ARG* 2.8 13.1 + - - +
93M SER 3.4 3.6 - - - +
95M ALA* 1.3 73.0 - - - +
97M ILE* 1.3 70.4 + - - +
99M ASP* 2.7 26.3 + - - +
100M GLU 3.0 8.3 + - - -
192M PRO* 2.6 32.8 + - + +
194M PRO* 3.5 28.1 - - - +
197M ALA* 3.5 9.3 - - - +
201M PHE* 3.9 6.7 - - + -
202M PHE* 3.5 22.9 - - + -
54N ASN* 5.2 4.9 + - - +
73N GLN* 5.4 0.4 + - - -
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Residues in contact with ILE 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81M PHE* 3.6 30.5 - - + -
93M SER 2.8 26.2 + - - +
94M LEU* 3.2 17.0 - - + +
96M ASN* 1.3 71.5 - - - +
98M PHE* 1.3 59.7 + - + +
100M GLU* 3.0 5.7 + - - +
101M TYR* 2.8 25.0 + - - +
115M LEU* 6.2 0.4 - - + -
118M TRP* 4.5 13.2 - - + -
168M TRP* 3.1 39.5 - - + -
192M PRO* 3.8 11.7 - - + -
201M PHE* 3.7 11.1 - - + -
207M PHE* 3.6 25.5 - - + -
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Residues in contact with PHE 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90M TRP* 4.2 19.5 - + - +
94M LEU* 2.9 33.8 + - + -
95M ALA* 3.4 9.9 - - - +
96M ASN 3.1 0.2 - - - -
97M ILE* 1.3 77.4 - - + +
99M ASP* 1.3 57.2 + - - +
101M TYR* 2.9 14.7 + + + +
102M THR* 2.8 31.2 + - - +
109M LEU* 4.1 14.8 - - + -
110M PRO* 3.6 33.2 - - + -
112M ASN 3.4 24.9 - - - -
113M GLY* 3.9 8.7 - - - -
115M LEU* 3.7 28.0 - - + -
118M TRP* 4.4 10.3 - + - -
226M LEU* 4.2 13.7 - - + -
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Residues in contact with ASP 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95M ALA* 2.9 15.7 + - - +
96M ASN* 2.7 23.2 + - - +
98M PHE* 1.3 71.2 - - - +
100M GLU* 1.3 60.1 + - - +
102M THR* 2.7 21.0 + - - -
103M ALA* 3.1 13.9 + - - +
109M LEU* 3.9 16.8 - - - +
202M PHE* 3.9 16.2 - - + -
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Residues in contact with GLU 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54K THR* 5.9 0.3 - - - +
96M ASN 3.0 5.1 + - - -
97M ILE 3.4 8.5 - - - +
99M ASP* 1.3 76.1 - - - +
101M TYR* 1.3 57.4 + - - +
103M ALA* 4.2 8.8 - - - +
104M ASP* 2.8 32.6 + - - +
201M PHE* 3.6 31.2 - - + +
202M PHE* 3.4 12.7 - - + +
203M GLY 3.0 23.9 + - - -
204M SER* 4.1 3.6 - - - +
205M ARG* 3.1 44.4 + - - -
206M PRO* 3.7 21.1 - - + -
207M PHE* 4.1 1.6 - - + -
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Residues in contact with TYR 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97M ILE 2.8 9.9 + - - +
98M PHE* 2.9 19.4 + + + +
100M GLU* 1.3 73.3 - - - +
102M THR* 1.3 79.1 + - + -
104M ASP* 3.2 1.4 + - - +
105M LEU* 3.0 47.6 + - + +
107M TYR* 3.3 20.3 + + + +
108M PRO 3.5 20.4 - - - -
110M PRO* 3.6 19.1 - - + -
118M TRP* 4.2 16.4 - + - -
207M PHE* 3.3 25.3 - + + -
224M TRP* 4.4 1.8 - - + -
225M ARG* 3.2 40.0 - - - -
226M LEU* 3.7 12.6 - - + -
227M PRO* 3.3 15.6 - - - +
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Residues in contact with THR 102 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47K SER* 4.5 2.8 + - - -
98M PHE 2.8 15.3 + - - +
99M ASP* 2.7 28.4 + - - -
101M TYR* 1.3 77.5 - - + +
103M ALA* 1.3 55.2 + - - +
105M LEU 2.3 25.9 - - - +
106M GLY* 4.5 1.4 - - - -
107M TYR 3.4 25.2 - - - +
108M PRO* 3.8 1.3 - - + -
109M LEU* 3.5 36.1 - - + +
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Residues in contact with ALA 103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47K SER* 2.9 35.5 + - - -
99M ASP 3.1 17.5 + - - +
100M GLU* 3.7 10.5 - - - +
102M THR* 1.3 76.7 + - - +
104M ASP* 1.3 62.0 + - - +
205M ARG* 3.9 23.3 + - - +
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Residues in contact with ASP 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47K SER* 4.8 3.6 - - - -
48K ASN* 5.4 4.9 + - - +
100M GLU* 2.8 21.6 + - - +
101M TYR 3.7 2.7 - - - +
103M ALA* 1.3 80.7 - - - +
105M LEU* 1.3 60.8 + - + +
205M ARG* 3.1 44.9 - - - +
206M PRO 3.6 0.2 - - - -
207M PHE* 3.2 15.3 + - + +
208M SER* 2.7 46.2 + - - -
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Residues in contact with LEU 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47K SER* 4.9 2.0 + - - -
101M TYR* 3.0 34.4 + - + +
102M THR 2.3 32.7 - - - +
103M ALA 4.0 1.3 - - - +
104M ASP* 1.3 78.6 - - + +
106M GLY* 1.3 59.5 + - - +
107M TYR* 3.2 45.5 + - + +
207M PHE* 4.2 9.4 - - + -
208M SER* 4.1 33.2 - - - +
211M ASN* 5.1 2.7 - - - +
224M TRP* 3.9 19.5 - - + -
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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