Contacts of the helix formed by residues 98 - 111 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C LEU 3.0 9.6 + - - +
95C ILE 3.2 4.7 + - - +
97C ARG* 1.3 113.3 + - - +
99C ARG* 1.3 58.1 + - - +
100C THR 3.4 2.5 - - - -
101C TYR* 3.3 11.3 + - + +
102C LEU* 2.9 32.8 + - + +
203C TYR* 2.7 38.4 + - + -
207C LEU* 3.4 10.4 - - + +
3115C EDO 4.4 11.2 + - - -
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Residues in contact with ARG 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ILE 2.9 10.1 + - - +
96C GLU* 3.2 30.7 + - - +
97C ARG 3.3 1.8 + - - -
98C ASP* 1.3 77.8 - - - +
100C THR* 1.3 57.5 + - - +
102C LEU* 3.9 0.7 - - - +
103C ALA* 3.0 29.5 + - - +
118C TYR* 2.8 67.3 + - + +
119C LEU* 4.0 7.5 + - - +
122C LEU* 3.9 24.7 - - + +
123C ASP* 3.7 29.0 + - - +
126C LEU* 4.4 18.9 - - + +
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Residues in contact with THR 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C PRO* 3.6 25.8 - - + +
10C ALA 3.7 19.1 - - - +
11C PRO* 4.5 3.8 - - + -
12C ASN* 5.3 1.8 - - + +
97C ARG 5.0 1.2 + - - -
98C ASP 3.4 0.6 - - - -
99C ARG* 1.3 77.7 - - - +
101C TYR* 1.3 62.1 + - - +
103C ALA 3.5 0.2 + - - -
104C ALA* 3.2 21.8 + - - +
114C TYR* 3.5 21.0 - - - +
118C TYR* 3.7 13.4 + - - -
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Residues in contact with TYR 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ASN* 5.7 6.7 - - + -
15C PRO* 3.9 20.0 - - + -
16C GLU* 2.6 34.1 + - + -
17C VAL* 4.2 2.9 - - - -
18C PHE* 3.4 22.2 + + - -
98C ASP* 3.3 9.3 + - + +
99C ARG 3.2 0.4 - - - -
100C THR* 1.3 77.3 - - - +
102C LEU* 1.3 69.3 + - + +
104C ALA* 3.1 7.5 + - - +
105C LEU* 2.9 44.1 + - + +
203C TYR* 3.8 41.9 - + - +
3115C EDO 3.4 28.5 - - - +
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Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ILE* 3.9 30.3 - - + +
98C ASP* 2.9 20.8 + - + +
101C TYR* 1.3 80.6 - - + +
103C ALA* 1.3 58.3 + - - +
105C LEU* 3.3 5.9 + - + +
106C GLU* 2.9 29.5 + - - +
122C LEU* 3.8 18.2 - - + -
172C LEU* 4.2 7.5 - - + +
200C THR* 4.0 33.0 - - + +
203C TYR* 3.8 26.7 - - + -
204C VAL* 4.3 7.0 - - + -
207C LEU* 4.3 20.2 - - + -
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Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C ARG 3.0 19.2 + - - +
100C THR 3.9 0.2 - - - +
101C TYR 3.2 0.2 - - - -
102C LEU* 1.3 76.3 - - - +
104C ALA* 1.3 58.3 + - - +
106C GLU* 3.4 0.6 + - - -
107C THR* 3.1 24.3 + - - -
114C TYR* 3.7 17.5 - - + -
117C SER* 3.4 15.0 - - - -
118C TYR* 3.6 35.0 - - + +
122C LEU* 3.7 10.9 - - + +
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Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ASN* 3.6 33.2 - - + +
15C PRO* 3.6 6.3 - - + -
100C THR 3.2 10.7 + - - +
101C TYR* 3.1 10.8 + - - +
103C ALA* 1.3 77.6 - - - +
105C LEU* 1.3 58.4 + - - +
107C THR 3.3 0.3 + - - -
108C LEU* 2.9 26.2 + - - +
114C TYR* 3.8 13.9 - - + -
335C PHE* 3.4 18.7 - - + -
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PRO* 3.9 20.8 - - + +
16C GLU 4.8 0.2 - - - +
17C VAL* 4.5 14.8 - - + -
101C TYR* 2.9 44.2 + - + +
102C LEU* 3.8 6.1 - - + +
104C ALA* 1.3 74.0 - - - +
106C GLU* 1.3 65.5 + - - +
108C LEU* 3.3 9.7 + - + +
109C ASP* 3.1 25.7 + - + +
199C LEU* 4.0 34.8 - - + +
200C THR* 3.6 30.1 - - + +
203C TYR* 4.5 7.0 - - + -
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Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LEU 2.9 18.1 + - - +
103C ALA* 3.6 6.7 - - - +
104C ALA 3.2 0.2 - - - -
105C LEU* 1.3 76.9 - - - +
107C THR* 1.3 57.3 + - - +
109C ASP* 4.2 2.0 - - - +
110C ASN* 2.8 36.0 + - + +
112C LYS* 4.4 13.7 - - + -
117C SER* 3.9 16.2 - - - +
121C ASP* 4.3 11.8 - - + +
122C LEU* 5.2 0.2 - - + -
171C PRO* 3.3 25.8 - - - +
172C LEU* 3.0 39.9 + - + +
197C THR* 5.7 0.2 - - - -
200C THR* 2.8 28.5 + - + +
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Residues in contact with THR 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ASN* 5.1 1.0 - - - +
43C SER* 5.2 0.3 + - - -
103C ALA 3.1 8.8 + - - -
104C ALA 3.6 4.0 - - - -
106C GLU* 1.3 76.3 - - - +
108C LEU* 1.3 62.6 + - - +
111C GLY* 2.8 27.1 + - - +
112C LYS 2.7 29.4 + - - +
114C TYR* 3.1 19.1 - - - +
117C SER* 2.9 16.7 + - - -
334C PRO* 3.6 25.3 - - + +
335C PHE* 3.7 24.0 - - + -
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Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLN 3.9 22.0 - - - +
14C GLN* 5.1 2.0 - - - -
15C PRO* 3.8 30.1 - - + +
41C ASN* 3.4 53.5 - - - +
42C PRO* 3.7 1.4 - - - +
48C ILE* 3.9 32.1 - - + -
104C ALA 2.9 17.0 + - - +
105C LEU* 3.3 16.1 + - + +
107C THR* 1.3 78.9 - - - +
109C ASP* 1.3 57.6 + - - +
335C PHE* 4.1 10.3 - - + -
3114C EDO 3.6 9.4 - - - +
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Residues in contact with ASP 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C THR* 2.7 13.3 + - - -
42C PRO* 3.5 7.6 - - - +
48C ILE* 3.4 11.9 - - + +
105C LEU 3.1 16.0 + - - +
106C GLU* 4.2 2.7 - - - +
108C LEU* 1.3 79.0 - - - +
110C ASN* 1.3 58.6 + - + +
196C GLN 3.4 7.8 - - - +
197C THR* 3.3 22.8 - - + +
198C PRO* 3.5 1.9 - - - +
199C LEU* 3.3 38.9 + - + +
200C THR* 4.9 2.4 + - + -
345C VAL* 5.0 1.7 - - - +
3703C NA 2.6 45.2 - - - -
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Residues in contact with ASN 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C PRO* 3.4 12.9 - - - +
106C GLU* 2.8 21.7 + - + +
109C ASP* 1.3 74.8 - - + +
111C GLY* 1.3 58.1 + - - +
112C LYS* 3.0 37.4 + - - +
168C TRP* 2.7 29.1 + - - -
169C ASN* 3.5 14.8 + - - +
171C PRO* 3.9 9.0 - - + +
197C THR* 3.8 14.2 - - + +
297C ASN* 4.5 1.6 + - - +
298C GLN* 4.7 2.6 + - - -
300C GLN* 5.0 6.5 + - - +
343C PRO 4.5 3.3 - - - +
345C VAL* 4.0 20.2 + - - +
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Residues in contact with GLY 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C PRO* 3.8 14.5 - - - +
43C SER* 4.5 4.3 - - - -
107C THR 2.8 17.0 + - - -
110C ASN* 1.3 78.1 - - - +
112C LYS* 1.3 65.5 + - - +
298C GLN* 4.5 3.8 - - - -
334C PRO* 3.2 15.7 - - - +
342C GLY* 3.5 4.5 - - - -
343C PRO* 3.3 23.1 - - - +
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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