Contacts of the helix formed by residues 98 - 111 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94L LEU 3.1 8.2 + - - +
95L ILE 3.2 5.6 - - - +
96L GLU 3.2 0.2 - - - -
97L ARG* 1.3 118.0 + - - +
99L ARG* 1.3 55.7 + - - +
100L THR 3.5 2.2 - - - -
101L TYR* 3.4 11.6 + - + -
102L LEU* 2.9 32.9 + - + +
203L TYR* 2.9 42.7 + - + -
207L LEU* 3.5 6.3 - - + +
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Residues in contact with ARG 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95L ILE* 2.9 11.4 + - + +
96L GLU* 3.3 29.2 + - - +
97L ARG 3.3 1.6 + - - -
98L ASP* 1.3 76.1 - - - +
100L THR* 1.3 65.3 + - - +
102L LEU 3.2 0.7 + - - -
103L ALA* 2.9 23.2 + - - +
118L TYR* 2.7 69.1 + - + +
119L LEU* 3.9 9.5 - - - +
122L LEU* 3.0 32.0 - - + +
123L ASP* 3.8 28.0 + - - +
126L LEU* 4.6 18.3 - - + +
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Residues in contact with THR 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L PRO* 3.8 22.7 - - + +
10L ALA 4.1 17.0 - - - +
11L PRO* 4.6 3.8 - - + -
12L ASN 5.4 1.8 - - - +
97L ARG 5.1 1.0 + - - -
98L ASP 3.5 0.2 - - - -
99L ARG* 1.3 76.5 - - - +
101L TYR* 1.3 62.8 + - - +
103L ALA 3.6 0.2 + - - -
104L ALA* 3.2 22.2 + - + +
114L TYR* 3.2 27.5 - - + +
118L TYR* 3.8 11.2 + - - -
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Residues in contact with TYR 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L ASN* 6.2 4.0 - - + -
15L PRO* 4.2 15.7 - - + -
16L GLU 2.6 32.7 + - - -
18L PHE* 3.2 32.5 + + - -
98L ASP* 3.4 14.2 + - + +
99L ARG 3.2 0.4 - - - -
100L THR* 1.3 78.7 - - - +
102L LEU* 1.3 62.9 + - + +
104L ALA* 3.1 7.4 + - - +
105L LEU* 2.9 51.6 + - + +
203L TYR* 3.8 43.3 - + - -
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Residues in contact with LEU 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95L ILE* 4.0 36.6 - - + +
98L ASP* 2.9 20.9 + - + +
101L TYR* 1.3 81.2 - - + +
103L ALA* 1.3 57.2 + - - +
105L LEU* 3.8 2.6 - - + +
106L GLU* 2.9 30.7 + - - +
122L LEU* 3.8 12.3 - - + -
172L LEU* 4.1 13.7 - - + +
200L THR* 3.9 40.4 - - + +
203L TYR* 3.8 32.8 - - + -
204L VAL* 4.5 5.8 - - + -
207L LEU* 4.3 6.3 - - + -
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Residues in contact with ALA 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99L ARG 2.9 18.1 + - - +
100L THR 3.8 0.7 - - - +
102L LEU* 1.3 75.4 - - - +
104L ALA* 1.3 62.9 + - - +
106L GLU 3.4 0.3 + - - -
107L THR* 3.1 26.3 + - - -
114L TYR* 3.6 19.3 - - + -
117L SER* 3.3 13.1 + - - -
118L TYR* 3.7 34.3 - - + +
122L LEU* 3.6 9.5 - - + +
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Residues in contact with ALA 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L ASN* 3.6 20.0 - - + +
15L PRO* 3.5 19.7 - - + -
100L THR 3.2 11.2 + - - +
101L TYR* 3.1 10.7 + - - +
103L ALA* 1.3 77.2 - - - +
105L LEU* 1.3 60.3 + - - +
107L THR* 3.3 4.0 + - - -
108L LEU* 2.9 28.4 + - - +
114L TYR* 3.5 17.7 - - + -
335L PHE* 3.6 9.0 - - + -
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Residues in contact with LEU 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L PRO* 3.9 16.3 - - + +
16L GLU 5.1 0.2 - - - +
17L VAL* 4.3 13.9 - - + -
101L TYR* 2.9 44.8 + - + +
102L LEU* 3.9 6.3 - - + +
104L ALA* 1.3 74.2 - - - +
106L GLU* 1.3 64.4 + - - +
108L LEU* 4.3 17.0 - - + -
109L ASP* 3.2 24.3 + - + +
199L LEU* 4.0 48.5 - - + +
200L THR* 3.8 14.9 - - + +
203L TYR* 4.7 4.5 - - + -
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Residues in contact with GLU 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102L LEU 2.9 19.6 + - - +
103L ALA* 3.5 2.0 - - - +
105L LEU* 1.3 78.1 - - - +
107L THR* 1.3 52.5 + - - +
109L ASP* 4.0 1.5 - - - +
110L ASN* 2.8 40.7 + - + +
112L LYS* 4.2 12.6 - - + -
117L SER* 3.2 21.5 - - - +
121L ASP* 4.3 11.6 - - + +
122L LEU* 5.2 0.4 - - + -
170L PHE 4.3 0.5 - - - -
171L PRO* 3.1 26.8 - - - +
172L LEU* 3.1 37.9 + - + +
173L LEU 4.8 0.2 + - - -
197L THR* 5.5 0.5 - - - -
200L THR* 2.9 27.0 + - + +
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Residues in contact with THR 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L ASN* 5.0 1.0 - - - +
43L SER* 5.2 0.2 + - - -
103L ALA 3.1 9.7 + - - -
104L ALA 3.5 8.1 - - - -
106L GLU* 1.3 79.2 - - - +
108L LEU* 1.3 60.0 + - - +
111L GLY* 2.8 27.5 + - - +
112L LYS* 3.0 29.6 + - - +
114L TYR* 3.1 23.3 - - - +
117L SER* 3.6 5.4 + - - -
334L PRO* 3.5 27.2 - - + +
335L PHE* 3.8 22.4 - - + -
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Residues in contact with LEU 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L GLN 3.4 26.0 - - - +
14L GLN* 4.5 5.6 - - + -
15L PRO* 3.8 26.5 - - + +
17L VAL* 5.4 0.2 - - + -
41L ASN* 3.2 55.7 - - - +
42L PRO* 3.5 1.0 - - - +
48L ILE* 3.8 33.2 - - + -
104L ALA 2.9 16.4 + - - +
105L LEU* 3.8 17.0 - - + +
106L GLU 3.4 0.2 - - - -
107L THR* 1.3 79.1 - - - +
109L ASP* 1.3 58.0 + - - +
334L PRO* 6.3 0.2 - - - -
335L PHE* 4.2 8.1 - - + -
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Residues in contact with ASP 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L THR* 2.6 14.7 + - - -
42L PRO* 3.5 8.1 - - - +
48L ILE* 3.2 17.7 - - + +
105L LEU* 3.2 16.2 + - + +
106L GLU* 4.2 2.0 - - - +
108L LEU* 1.3 79.8 - - + +
110L ASN* 1.3 58.4 + - - +
196L GLN 3.4 6.2 - - - +
197L THR* 3.1 27.0 - - + +
198L PRO* 3.3 10.9 - - - +
199L LEU* 3.5 21.1 + - + +
200L THR* 5.0 1.9 + - + -
345L VAL* 5.1 0.9 - - - +
3712L NA 2.6 44.7 - - - -
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Residues in contact with ASN 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L PRO* 3.6 14.2 - - - +
106L GLU* 2.8 25.1 + - + +
109L ASP* 1.3 75.5 - - - +
111L GLY* 1.3 54.6 + - - +
112L LYS* 3.0 38.1 + - - +
168L TRP* 2.7 33.7 + - - -
169L ASN* 3.4 14.5 + - - +
171L PRO* 3.8 7.6 - - + +
197L THR* 3.8 12.4 - - + +
297L ASN* 4.3 1.6 - - - +
298L GLN* 4.4 3.5 + - - -
300L GLN* 4.9 7.1 + - - +
343L PRO 4.6 1.9 - - - +
345L VAL* 4.0 16.9 + - - +
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Residues in contact with GLY 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L PRO* 4.4 3.3 - - - +
43L SER* 4.5 4.7 - - - -
107L THR 2.8 20.5 + - - -
109L ASP 3.9 0.2 - - - -
110L ASN* 1.3 73.6 - - - +
112L LYS* 1.3 67.1 + - - +
298L GLN* 4.6 4.5 - - - -
334L PRO* 3.3 15.6 - - - +
342L GLY* 3.6 4.3 - - - -
343L PRO* 3.4 32.3 - - - +
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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