Contacts of the helix formed by residues 98 - 111 (chain A) in PDB entry 1ZUM
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 ASP 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LEU 3.0 8.8 + - - +
95A ILE 3.1 5.8 + - - +
97A ARG* 1.3 116.0 + - - +
99A ARG* 1.3 58.0 + - - +
100A THR 3.5 2.0 - - - -
101A TYR* 3.4 12.0 + - + +
102A LEU* 2.9 32.0 + - + +
203A TYR* 2.6 43.0 + - + -
207A LEU* 3.7 3.7 - - + +
3111A EDO 4.3 12.6 + - - -
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Residues in contact with ARG 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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95A ILE 2.9 8.8 + - - +
96A GLU* 3.2 29.4 + - - +
97A ARG 3.3 1.4 + - - -
98A ASP* 1.3 78.6 - - - +
100A THR* 1.3 59.0 + - - +
102A LEU* 3.7 0.9 - - - +
103A ALA* 2.8 32.6 + - - +
118A TYR* 2.7 67.7 + - + +
119A LEU* 3.9 8.5 - - - +
122A LEU* 3.8 25.8 - - + +
123A ASP* 3.8 29.5 + - - +
126A LEU* 4.3 19.6 - - + +
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Residues in contact with THR 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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9A PRO* 3.7 17.1 - - + +
10A ALA 3.9 17.9 - - - +
11A PRO* 4.7 3.4 - - + -
12A ASN 5.4 2.0 - - - +
97A ARG 5.2 0.6 + - - -
98A ASP 3.5 0.6 - - - -
99A ARG* 1.3 76.5 - - - +
101A TYR* 1.3 63.9 + - - +
103A ALA* 3.5 1.9 + - - +
104A ALA* 3.2 22.3 + - - +
114A TYR* 3.4 19.6 - - + +
118A TYR* 3.6 21.7 + - - -
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Residues in contact with TYR 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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12A ASN* 6.3 2.5 - - + -
15A PRO* 3.9 20.0 - - + -
16A GLU 2.6 31.5 + - - -
17A VAL* 4.1 3.1 - - - -
18A PHE* 3.5 23.4 + + - -
98A ASP* 3.4 9.7 + - - +
99A ARG 3.3 0.4 - - - -
100A THR* 1.3 78.6 - - - +
102A LEU* 1.3 61.8 + - + +
104A ALA* 3.2 7.8 + - - +
105A LEU* 2.9 50.9 + - + +
203A TYR* 3.8 45.5 - + - -
3111A EDO 3.7 25.4 - - - +
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Residues in contact with LEU 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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95A ILE* 4.1 27.6 - - + +
98A ASP 2.9 23.3 + - - +
99A ARG 3.8 2.5 - - - +
101A TYR* 1.3 78.4 - - + +
103A ALA* 1.3 57.7 + - - +
105A LEU* 3.3 4.1 + - + +
106A GLU* 2.8 31.4 + - - +
122A LEU* 4.3 8.5 - - + -
172A LEU* 4.1 12.7 - - + +
200A THR* 3.9 26.4 - - + +
203A TYR* 3.5 43.3 - - + -
204A VAL* 4.4 9.6 - - + -
207A LEU* 4.3 12.3 - - + -
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Residues in contact with ALA 103 (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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99A ARG 2.8 20.9 + - - +
100A THR 3.8 0.7 - - - +
101A TYR 3.3 0.2 - - - -
102A LEU* 1.3 73.7 - - - +
104A ALA* 1.3 57.6 + - - +
106A GLU* 3.5 0.6 + - - -
107A THR* 3.2 23.9 + - - -
114A TYR* 3.8 12.1 - - + -
117A SER* 3.3 16.2 - - - -
118A TYR* 3.7 41.7 - - + +
122A LEU* 3.9 11.8 - - + +
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Residues in contact with ALA 104 (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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12A ASN* 3.6 32.1 - - + +
15A PRO* 4.2 8.1 - - + -
100A THR 3.2 12.1 + - - +
101A TYR* 3.2 10.8 + - - +
103A ALA* 1.3 74.6 - - - +
105A LEU* 1.3 59.8 + - - +
107A THR* 3.2 3.3 + - - -
108A LEU* 2.9 30.0 + - - +
114A TYR* 3.8 14.5 - - + -
335A PHE* 3.6 12.1 - - + -
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Residues in contact with LEU 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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15A PRO* 4.0 21.5 - - + +
17A VAL* 4.3 15.9 - - + -
101A TYR* 2.9 45.5 + - + +
102A LEU* 3.3 7.8 + - + +
104A ALA* 1.3 76.3 - - - +
106A GLU* 1.3 61.5 + - - +
108A LEU* 3.6 6.7 - - + +
109A ASP* 3.1 24.4 + - - +
199A LEU* 4.0 49.1 - - + +
200A THR* 3.9 13.2 - - + -
203A TYR* 4.6 5.6 - - + -
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Residues in contact with GLU 106 (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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102A LEU 2.8 17.2 + - - +
103A ALA* 3.6 8.3 - - - +
105A LEU* 1.3 77.9 - - - +
107A THR* 1.3 57.7 + - - +
109A ASP* 3.8 1.6 - - - +
110A ASN* 2.8 36.4 + - + +
112A LYS* 4.2 13.7 - - + -
117A SER* 4.0 13.9 - - - +
121A ASP* 4.1 12.4 - - + +
122A LEU* 5.3 0.7 - - + -
171A PRO* 3.3 24.2 - - + +
172A LEU* 3.0 37.4 + - + +
200A THR* 2.8 34.0 + - + +
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Residues in contact with THR 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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43A SER* 5.1 1.0 + - - -
103A ALA 3.2 5.8 + - - -
104A ALA 3.2 6.9 + - - -
106A GLU* 1.3 78.5 - - - +
108A LEU* 1.3 60.9 + - - +
111A GLY* 2.7 28.7 + - - +
112A LYS 2.8 28.6 + - - +
114A TYR* 3.0 25.1 - - - +
117A SER* 3.0 8.3 + - - -
334A PRO* 3.5 22.9 - - + +
335A PHE* 3.6 26.2 - - + -
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Residues in contact with LEU 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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13A GLN 3.7 23.3 - - - +
14A GLN* 4.9 3.8 - - + -
15A PRO* 3.8 29.4 - - + +
17A VAL* 5.4 0.2 - - + -
41A ASN* 3.3 54.7 - - - +
42A PRO* 3.6 1.0 - - - +
48A ILE* 4.0 31.6 - - + -
104A ALA 2.9 16.2 + - - +
105A LEU* 3.6 13.0 - - + +
106A GLU 3.3 0.2 - - - -
107A THR* 1.3 78.6 - - - +
109A ASP* 1.3 57.6 + - - +
334A PRO* 6.3 0.2 - - - -
335A PHE* 4.0 10.5 - - + -
3110A EDO 3.6 9.2 - - - +
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Residues in contact with ASP 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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39A THR* 2.8 10.1 + - - +
42A PRO* 3.5 8.1 - - - +
48A ILE* 3.2 13.5 - - + +
105A LEU 3.1 16.7 + - - +
106A GLU* 4.2 2.2 - - - +
108A LEU* 1.3 78.0 - - - +
110A ASN* 1.3 58.1 + - - +
196A GLN 3.4 7.5 - - - +
197A THR* 3.5 15.3 - - + +
198A PRO* 3.6 2.8 - - - +
199A LEU* 3.1 47.4 + - + +
200A THR* 4.9 2.0 + - + +
345A VAL* 5.1 2.3 - - - +
3701A NA 2.6 45.7 - - - -
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Residues in contact with ASN 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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42A PRO* 3.5 12.5 - - - +
106A GLU* 2.8 23.7 + - + +
109A ASP* 1.3 73.9 - - + +
111A GLY* 1.3 56.0 + - - +
112A LYS* 3.0 38.9 + - - +
168A TRP* 2.8 29.5 + - - -
169A ASN* 3.6 12.3 + - - +
171A PRO* 4.0 7.7 - - + +
197A THR* 4.0 13.0 - - + +
297A ASN* 4.4 2.1 - - - +
298A GLN* 4.4 3.5 + - - -
300A GLN* 5.0 6.6 + - - +
343A PRO 4.7 2.3 - - - +
345A VAL* 4.1 21.3 + - - +
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Residues in contact with GLY 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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42A PRO* 3.8 13.4 - - - +
43A SER* 4.5 3.6 - - - -
107A THR 2.7 21.6 + - - -
110A ASN* 1.3 73.8 - - - +
112A LYS* 1.3 65.9 + - - +
298A GLN* 4.4 4.0 - - - -
334A PRO* 3.3 15.3 - - - +
342A GLY* 3.5 5.4 - - - -
343A PRO* 3.4 24.1 - - - +
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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