Contacts of the helix formed by residues 93 - 111 (chain A) in PDB entry 5ZUN
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 PHE 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL* 4.0 6.9 - - - +
92A ASP* 1.3 73.0 + - - +
94A HIS* 1.3 62.3 + - - +
96A PHE* 3.0 39.5 + + - +
97A VAL* 3.9 2.7 + - + -
123A MET* 3.7 26.7 - - + -
126A ALA* 4.5 2.5 - - + -
127A ILE* 3.6 35.4 - - + -
130A LEU* 3.9 24.2 - - + -
209A PHE* 5.6 0.2 - + - -
212A GLN* 2.9 42.7 + - + +
213A LEU* 4.2 5.8 - - + -
216A ALA* 3.6 32.1 - - + +
219A ARG* 3.9 9.9 - - - +
411A CL 4.3 3.6 - - + -
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Residues in contact with HIS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASP* 2.9 17.6 + - + +
93A PHE* 1.3 75.6 - - - +
95A VAL* 1.3 65.6 - - - +
97A VAL* 3.0 13.7 + - + +
98A ARG* 2.8 43.0 + - + +
134A GLU* 2.8 33.0 + - - -
219A ARG* 3.6 2.9 - - - +
411A CL 3.5 24.7 - - + -
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASN* 4.6 1.8 - - - +
26A ASP* 4.2 13.2 - - - +
28A GLN* 5.1 1.8 - - - +
78A VAL* 3.8 23.6 - - + -
90A VAL* 3.7 7.2 - - + -
91A SER* 3.5 22.0 - - - +
92A ASP* 3.0 21.9 + - + +
94A HIS* 1.3 75.2 - - - +
96A PHE* 1.3 63.2 + - - +
98A ARG* 3.6 30.2 - - - +
99A ASP* 3.0 34.1 + - - +
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Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A HIS* 3.8 24.5 + - + +
78A VAL* 3.6 41.7 - - + -
80A HIS* 4.4 2.9 - + - -
89A VAL 5.0 0.7 - - - -
90A VAL* 3.8 24.2 - - + -
93A PHE* 3.0 51.0 + + - +
95A VAL* 1.3 78.2 - - - +
97A VAL* 1.3 57.3 + - - +
99A ASP* 3.5 5.2 + - - +
100A VAL* 3.0 33.1 + - - +
123A MET* 3.9 17.0 - - + -
127A ILE* 3.6 25.8 - - + -
209A PHE* 3.9 14.6 - + - -
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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
----------------------------------------------------------
93A PHE* 4.5 7.2 - - + +
94A HIS* 3.0 13.8 + - + +
96A PHE* 1.3 74.6 - - - +
98A ARG* 1.3 66.9 + - - +
100A VAL* 3.2 3.7 + - - +
101A LEU* 2.9 28.4 + - + +
127A ILE* 4.1 15.7 - - + +
130A LEU* 3.7 28.5 - - + +
131A THR* 3.7 30.5 - - - +
134A GLU* 3.7 22.7 - - - +
411A CL 4.2 13.2 - - + -
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Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASN* 3.4 20.0 - - - +
25A ALA* 3.9 24.4 - - + +
26A ASP* 2.9 39.2 + - - +
94A HIS* 2.8 33.9 + - + +
95A VAL* 3.6 23.2 + - - +
97A VAL* 1.3 78.9 - - - +
99A ASP* 1.3 79.2 + - - +
101A LEU* 3.2 10.4 + - - +
102A GLN* 2.9 27.5 + - + +
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Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 5.0 1.8 - - + +
24A ASN* 2.9 38.2 + - + +
25A ALA 4.4 0.7 + - - -
30A LEU* 3.6 21.2 - - + +
75A HIS* 3.4 14.3 - - - +
77A HIS* 6.2 0.4 - - - +
78A VAL* 4.6 5.5 + - - +
95A VAL* 3.0 25.6 + - - +
96A PHE* 3.9 4.8 - - - +
98A ARG* 1.3 103.4 + - - +
100A VAL* 1.3 67.1 + - - +
102A GLN* 3.3 10.0 + - - +
103A HIS* 3.1 17.5 + - - +
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.6 41.0 - - + -
48A SER* 5.3 0.2 - - - -
75A HIS* 3.8 7.2 - - - +
77A HIS* 4.2 9.6 - - + -
96A PHE 3.0 16.4 + - - +
97A VAL 3.6 5.8 - - - +
99A ASP* 1.3 75.9 - - - +
101A LEU* 1.3 57.4 + - - +
103A HIS* 3.2 2.9 + - - +
104A VAL* 2.9 34.9 + - + +
118A LEU* 4.5 4.5 - - + -
127A ILE* 3.8 18.4 - - + -
128A ALA* 6.4 0.7 - - - -
131A THR* 3.9 26.5 - - + +
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Residues in contact with LEU 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* 2.9 23.3 + - + +
98A ARG* 3.6 10.3 - - - +
100A VAL* 1.3 77.3 - - - +
102A GLN* 1.3 58.1 + - - +
104A VAL* 3.9 4.0 - - + +
105A ASP* 2.8 36.7 + - - +
131A THR* 3.6 24.5 - - + +
134A GLU* 3.3 40.4 - - + +
135A ARG* 3.8 46.0 - - + +
139A PHE* 4.3 9.0 - - + -
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Residues in contact with GLN 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.0 18.0 - - + +
23A VAL 2.9 24.4 + - - +
24A ASN* 3.3 26.3 - - - +
25A ALA* 4.0 4.7 + - - +
98A ARG* 2.9 14.8 + - + +
99A ASP* 3.5 11.5 - - - +
100A VAL 3.2 0.2 - - - -
101A LEU* 1.3 75.8 - - - +
103A HIS* 1.3 58.6 + - - +
105A ASP* 3.8 5.4 - - - +
106A SER* 2.9 32.2 + - - -
407A EDO 5.9 0.4 + - - -
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Residues in contact with HIS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.6 10.5 - - + +
32A CYS* 3.6 12.6 - - - -
34A TYR* 2.7 36.1 + + - -
46A PHE* 3.7 7.7 - - + -
73A PHE* 3.7 18.7 - + - -
74A ALA 3.4 26.5 - - - -
75A HIS* 2.9 30.9 + - + +
99A ASP 3.1 5.9 + - - +
100A VAL 3.7 6.5 - - - +
102A GLN* 1.3 76.8 - - - +
104A VAL* 1.3 65.2 + - - +
106A SER* 3.3 3.7 + - - -
107A MET* 3.0 21.9 + - + +
407A EDO 3.6 20.2 - - - -
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 4.3 9.9 - - + -
73A PHE* 4.0 21.3 - - + -
100A VAL* 2.9 34.7 + - + +
101A LEU* 3.9 7.2 - - + +
103A HIS* 1.3 75.7 - - - +
105A ASP* 1.3 60.7 + - - +
107A MET* 3.3 2.1 + - - +
108A GLN* 2.8 53.5 + - + +
116A VAL* 4.3 6.1 - - + -
118A LEU* 4.6 0.7 - - + -
138A HIS* 4.3 2.5 - - - +
139A PHE* 3.9 33.4 - - + -
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Residues in contact with ASP 105 (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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101A LEU* 2.8 26.9 + - - +
102A GLN* 3.8 5.5 - - - +
104A VAL* 1.3 78.5 - - - +
106A SER* 1.3 62.6 + - - +
108A GLN* 4.0 8.4 - - - +
109A LYS* 3.2 26.3 + - - +
135A ARG* 2.8 44.5 + - - -
138A HIS* 4.8 1.0 + - - -
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLN* 2.9 20.8 + - - -
103A HIS* 3.8 2.5 - - - -
105A ASP* 1.3 78.2 - - - +
107A MET* 1.3 59.3 + - - +
109A LYS* 3.3 35.3 + - - +
110A ASP* 3.4 12.8 + - - +
407A EDO 2.7 38.8 + - - -
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Residues in contact with MET 107 (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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34A TYR* 3.4 36.3 - - + -
44A LEU* 3.6 23.3 - - + -
71A LEU* 4.0 11.9 - - + -
73A PHE* 3.8 30.5 - - + -
103A HIS* 3.0 16.8 + - - +
104A VAL 3.7 3.1 - - - +
106A SER* 1.3 75.0 - - - +
108A GLN* 1.3 65.6 + - - +
110A ASP* 3.0 13.5 + - - -
111A TYR* 3.1 43.1 + - - -
407A EDO 4.0 12.0 + - - +
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Residues in contact with GLN 108 (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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44A LEU* 4.0 22.0 - - + -
104A VAL* 2.8 33.5 + - + +
105A ASP* 4.1 8.0 - - - +
107A MET* 1.3 73.9 - - - +
109A LYS* 1.3 62.5 + - - +
111A TYR 3.1 23.0 - - - +
112A PRO* 3.1 6.4 - - - +
113A GLY 6.1 0.4 - - - +
114A LEU 3.9 15.0 + - - +
116A VAL* 3.5 23.5 - - + +
138A HIS* 2.6 38.3 + - - -
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Residues in contact with LYS 109 (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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105A ASP 3.2 12.0 + - - +
106A SER* 3.3 32.6 + - - +
108A GLN* 1.3 78.3 - - - +
110A ASP* 1.3 83.4 + - - +
111A TYR 3.4 0.2 - - - -
112A PRO* 3.6 15.3 - - - +
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Residues in contact with ASP 110 (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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106A SER* 3.4 6.3 + - - +
107A MET* 3.0 9.4 + - - +
109A LYS* 1.3 106.1 + - - +
111A TYR* 1.3 77.0 + - + +
112A PRO* 3.3 8.1 - - - +
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Residues in contact with TYR 111 (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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41A PRO* 3.9 17.9 - - + -
44A LEU* 4.0 12.9 - - + +
71A LEU* 3.4 22.6 - - + +
107A MET* 3.1 41.3 + - + +
108A GLN* 3.1 10.4 + - - +
110A ASP* 1.3 90.9 - - + +
112A PRO* 1.3 69.5 - - - +
114A LEU* 3.2 42.6 + - + +
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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
------------------------------------------------------------
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