Contacts of the helix formed by residues 98 - 111 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317D GLU* 4.6 1.6 - - - +
321D ARG* 3.9 9.0 + - - -
94F LEU 3.0 9.6 + - - +
95F ILE 3.1 4.9 + - - +
97F ARG* 1.3 116.3 + - - +
99F ARG* 1.3 57.5 + - - +
100F THR 3.5 2.0 - - - -
101F TYR* 3.3 6.5 + - + +
102F LEU* 2.9 33.0 + - + +
203F TYR* 2.7 42.3 + - + -
207F LEU* 3.6 4.6 - - + +
3122F EDO 4.1 13.9 + - - -
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Residues in contact with ARG 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F ILE 2.8 10.3 + - - +
96F GLU* 3.2 33.6 + - - +
97F ARG 3.4 1.4 + - - -
98F ASP* 1.3 76.5 - - - +
100F THR* 1.3 63.4 + - - +
102F LEU* 3.3 0.9 + - - +
103F ALA* 2.9 27.4 + - - +
118F TYR* 2.9 67.2 + - + +
119F LEU* 4.1 8.1 + - - +
122F LEU* 3.9 25.6 - - + +
123F ASP* 3.7 30.7 + - - +
126F LEU* 4.6 14.2 - - + +
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Residues in contact with THR 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F PRO* 3.7 26.5 - - + +
10F ALA 3.9 16.6 - - - +
11F PRO* 4.8 3.4 - - + -
12F ASN 5.5 1.6 - - - +
97F ARG 5.2 0.8 + - - -
98F ASP 3.5 0.2 - - - -
99F ARG* 1.3 76.7 - - - +
101F TYR* 1.3 63.8 + - - +
103F ALA* 3.5 1.9 + - - +
104F ALA* 3.2 22.2 + - - +
114F TYR* 3.4 19.6 - - + +
118F TYR* 3.7 13.3 + - - -
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Residues in contact with TYR 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ASN* 5.9 3.6 - - + -
15F PRO* 3.8 20.6 - - + -
16F GLU* 2.6 31.7 + - + -
17F VAL* 4.0 3.1 - - - -
18F PHE* 3.4 24.5 + + - -
98F ASP* 3.3 8.1 + - - +
99F ARG 3.3 0.2 - - - -
100F THR* 1.3 80.0 - - - +
102F LEU* 1.3 62.7 + - + +
104F ALA* 3.1 7.5 + - - +
105F LEU* 2.9 52.2 + - + +
203F TYR* 3.8 38.9 - + - +
3122F EDO 3.4 31.0 - - - +
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Residues in contact with LEU 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F ILE* 3.9 33.9 - - + +
98F ASP* 2.9 20.5 + - + +
99F ARG 3.9 2.0 - - - +
101F TYR* 1.3 81.2 - - + +
103F ALA* 1.3 58.1 + - - +
105F LEU* 3.2 2.8 + - + +
106F GLU* 2.8 31.2 + - - +
122F LEU* 3.9 14.4 - - + -
172F LEU* 4.1 7.0 - - + +
200F THR* 3.9 35.7 - - + +
203F TYR* 3.7 27.8 - - + -
204F VAL* 4.2 15.3 - - + -
207F LEU* 4.3 9.6 - - + -
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Residues in contact with ALA 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F ARG 2.9 17.5 + - - +
102F LEU* 1.3 76.7 - - - +
104F ALA* 1.3 61.6 + - - +
106F GLU* 3.5 0.6 + - - -
107F THR* 3.1 20.6 + - - -
114F TYR* 3.6 20.6 - - + -
117F SER* 3.3 14.5 - - - -
118F TYR* 3.6 25.8 - - + +
122F LEU* 3.4 20.8 - - + +
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Residues in contact with ALA 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ASN* 3.5 32.5 - - + +
15F PRO* 4.1 7.2 - - + -
100F THR 3.2 11.2 + - - +
101F TYR* 3.1 10.2 + - - +
103F ALA* 1.3 76.6 - - - +
105F LEU* 1.3 60.8 + - - +
107F THR 3.3 1.0 + - - -
108F LEU* 2.9 26.3 + - - +
114F TYR* 3.7 13.2 - - + -
335F PHE* 3.5 18.5 - - + -
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Residues in contact with LEU 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F PRO* 3.9 21.7 - - + +
16F GLU 4.8 0.2 - - - +
17F VAL* 4.4 16.6 - - + -
101F TYR* 2.9 47.6 + - + +
102F LEU* 3.8 6.3 - - + +
104F ALA* 1.3 77.4 - - - +
106F GLU* 1.3 63.6 + - - +
108F LEU* 3.3 8.8 + - + +
109F ASP* 3.1 24.1 + - - +
199F LEU* 4.1 42.4 - - + +
200F THR* 3.8 18.6 - - + -
203F TYR* 4.6 5.2 - - + -
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Residues in contact with GLU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F LEU 2.8 17.8 + - - +
103F ALA* 3.6 7.2 - - - +
105F LEU* 1.3 76.7 - - - +
107F THR* 1.3 57.1 + - - +
109F ASP* 4.2 1.6 - - - +
110F ASN* 2.8 36.6 + - - +
112F LYS* 4.2 15.3 - - + -
117F SER* 3.9 15.3 - - - +
121F ASP* 4.1 12.2 - - + +
122F LEU* 5.4 0.4 - - + -
171F PRO* 3.4 25.8 - - + +
172F LEU* 3.0 36.0 + - + +
197F THR* 5.6 0.3 - - - -
200F THR* 2.7 31.1 + - + +
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Residues in contact with THR 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F ASN* 5.1 1.0 - - - +
43F SER* 5.2 0.2 + - - -
103F ALA 3.1 8.9 + - - -
104F ALA 3.3 4.0 + - - -
106F GLU* 1.3 79.3 - - - +
108F LEU* 1.3 59.4 + - - +
111F GLY* 2.8 27.7 + - - +
112F LYS 2.8 28.5 + - - +
114F TYR* 3.1 17.3 - - - +
117F SER* 3.0 18.0 + - - -
334F PRO* 3.7 21.1 - - + +
335F PHE* 3.6 28.7 - - + -
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Residues in contact with LEU 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F GLN 3.7 22.4 - - - +
14F GLN* 4.2 13.5 - - - +
15F PRO* 4.0 26.9 - - + +
41F ASN* 3.2 56.6 - - - +
42F PRO* 3.5 1.6 - - - +
48F ILE* 4.0 31.6 - - + -
104F ALA 2.9 16.3 + - - +
105F LEU* 3.3 12.8 + - + +
107F THR* 1.3 76.1 - - - +
109F ASP* 1.3 61.1 + - - +
335F PHE* 4.0 11.2 - - + -
3121F EDO 3.8 4.7 - - - +
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Residues in contact with ASP 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F THR* 2.7 12.9 + - - -
42F PRO* 3.5 8.1 - - - +
48F ILE* 3.4 12.6 - - + +
105F LEU 3.1 14.0 + - - +
106F GLU* 4.2 2.7 - - - +
108F LEU* 1.3 81.2 - - + +
110F ASN* 1.3 58.5 + - + +
196F GLN 3.5 7.1 - - - +
197F THR* 3.3 24.0 - - + +
198F PRO* 3.4 2.3 - - - +
199F LEU* 3.4 38.1 + - + +
200F THR* 5.0 2.0 + - + +
345F VAL* 5.0 2.4 - - - +
3706F NA 2.4 46.9 - - - -
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Residues in contact with ASN 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F PRO* 3.5 11.6 - - - +
106F GLU* 2.8 24.5 + - + +
109F ASP* 1.3 74.6 - - + +
111F GLY* 1.3 55.4 + - - +
112F LYS* 2.9 36.8 + - - +
168F TRP* 2.8 29.3 + - - -
169F ASN* 3.4 15.2 + - - +
171F PRO* 4.0 8.3 - - + +
197F THR* 3.8 14.7 - - + +
297F ASN* 4.5 1.8 + - - +
298F GLN* 4.7 2.6 + - - -
300F GLN* 5.0 7.2 + - - +
343F PRO 4.6 2.4 - - - +
345F VAL* 4.0 21.5 + - - +
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Residues in contact with GLY 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F PRO* 3.8 15.1 - - - +
43F SER* 4.5 3.4 - - - -
107F THR 2.8 21.6 + - - -
110F ASN* 1.3 73.3 - - - +
112F LYS* 1.3 67.1 + - - +
298F GLN* 4.5 4.0 - - - -
334F PRO* 3.2 15.1 - - - +
342F GLY* 3.5 4.7 - - - -
343F PRO* 3.4 23.7 - - - +
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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