Contacts of the helix formed by residues 98 - 111 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367D LEU* 5.2 2.3 - - - +
3126D EDO 3.8 14.5 + - - -
94H LEU 3.1 9.9 + - - +
95H ILE 3.3 4.9 - - - +
97H ARG* 1.3 115.6 + - - +
99H ARG* 1.3 57.4 + - - +
100H THR 3.4 2.2 - - - -
101H TYR* 3.3 11.6 + - + +
102H LEU* 2.9 32.1 + - + +
203H TYR* 2.6 42.3 + - + +
207H LEU* 3.6 3.9 - - + +
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Residues in contact with ARG 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H ILE 2.9 10.4 + - - +
96H GLU* 3.2 31.4 + - - +
97H ARG 3.2 1.8 + - - +
98H ASP* 1.3 76.3 - - - +
100H THR* 1.3 58.1 + - - +
102H LEU* 3.3 0.9 + - - +
103H ALA* 2.9 33.1 + - - +
118H TYR* 2.7 66.9 + - + +
119H LEU* 3.9 9.7 + - - +
122H LEU* 3.8 24.4 - - + +
123H ASP* 3.8 29.8 + - - +
126H LEU* 4.4 17.6 - - + +
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Residues in contact with THR 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382D GLN* 5.5 4.6 + - - +
9H PRO* 3.7 17.5 - - + +
10H ALA 4.1 15.9 - - - +
11H PRO* 4.7 3.6 - - + -
12H ASN* 5.4 2.7 - - + +
97H ARG 5.0 0.8 + - - -
98H ASP 3.4 0.8 - - - -
99H ARG* 1.3 76.4 - - - +
101H TYR* 1.3 64.8 + - - +
103H ALA* 3.4 1.9 + - - +
104H ALA* 3.1 22.7 + - - +
114H TYR* 3.4 19.1 - - + +
118H TYR* 3.5 22.1 + - - -
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Residues in contact with TYR 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D LYS* 5.6 0.4 - - - -
3126D EDO 3.6 46.0 - - - -
12H ASN* 6.3 3.8 - - + -
15H PRO* 3.8 21.5 - - + -
16H GLU 2.7 31.2 + - - -
17H VAL* 4.1 3.6 - - - -
18H PHE* 3.5 13.6 + + - -
98H ASP* 3.3 10.1 + - + +
99H ARG 3.3 0.2 - - - -
100H THR* 1.3 80.2 - - - +
102H LEU* 1.3 62.4 + - + +
104H ALA* 3.3 5.4 + - - +
105H LEU* 2.9 52.4 + - + +
203H TYR* 3.8 36.4 - + - -
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Residues in contact with LEU 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H ILE* 3.9 29.8 - - + +
98H ASP* 2.9 23.6 + - + +
99H ARG 3.9 2.5 - - - +
101H TYR* 1.3 77.2 - - + +
103H ALA* 1.3 58.2 + - - +
105H LEU* 3.3 3.4 + - + +
106H GLU* 2.9 30.1 + - - +
122H LEU* 4.2 13.0 - - + -
172H LEU* 4.2 9.3 - - + +
200H THR* 3.8 35.9 - - + +
203H TYR* 3.7 27.6 - - + -
204H VAL* 4.4 7.2 - - + -
207H LEU* 4.3 21.3 - - + -
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Residues in contact with ALA 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H ARG 2.9 17.9 + - - +
100H THR 3.8 0.9 - - - +
102H LEU* 1.3 76.2 - - - +
104H ALA* 1.3 61.7 + - - +
106H GLU* 3.4 1.2 + - - -
107H THR* 3.1 26.5 + - - -
114H TYR* 3.8 16.4 - - + -
117H SER* 3.4 10.7 - - - -
118H TYR* 3.7 37.0 - - + +
122H LEU* 4.0 8.4 - - + +
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Residues in contact with ALA 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ASN* 3.4 32.3 - - + +
15H PRO* 4.1 8.1 - - + -
100H THR 3.1 17.0 + - - +
101H TYR* 3.7 4.7 - - - +
103H ALA* 1.3 73.1 - - - +
105H LEU* 1.3 62.3 + - - +
107H THR 3.2 1.4 + - - -
108H LEU* 2.8 29.6 + - - +
114H TYR* 3.7 9.5 - - + -
335H PHE* 3.5 21.0 - - + -
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Residues in contact with LEU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H PRO* 4.0 19.9 - - + +
17H VAL* 4.1 27.1 - - + -
101H TYR* 2.9 48.1 + - + +
102H LEU* 3.8 6.1 - - + +
104H ALA* 1.3 76.7 - - - +
106H GLU* 1.3 62.9 + - - +
108H LEU* 3.3 8.4 + - + +
109H ASP* 3.1 24.3 + - + +
199H LEU* 4.1 33.9 - - + +
200H THR* 3.8 20.1 - - + +
203H TYR* 4.6 6.3 - - + -
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Residues in contact with GLU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H LEU 2.9 17.6 + - - +
103H ALA* 3.5 8.1 - - - +
104H ALA 3.2 0.2 - - - -
105H LEU* 1.3 77.8 - - - +
107H THR* 1.3 58.3 + - - +
109H ASP* 4.2 1.9 - - - +
110H ASN* 2.8 36.6 + - + +
112H LYS* 4.1 14.6 - - + -
117H SER* 3.9 14.6 - - - +
121H ASP* 4.2 10.5 - - + +
122H LEU* 5.3 0.2 - - + -
171H PRO* 3.3 23.4 - - + +
172H LEU* 3.0 42.0 + - + +
200H THR* 2.8 28.2 + - + +
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Residues in contact with THR 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H ASN* 5.2 0.9 - - - +
43H SER* 5.2 0.3 + - - -
103H ALA 3.1 5.7 + - - -
104H ALA 3.5 7.4 - - - -
106H GLU* 1.3 79.5 - - - +
108H LEU* 1.3 59.1 + - - +
111H GLY* 2.9 27.3 + - - +
112H LYS 2.8 29.1 + - - +
114H TYR* 3.1 19.7 - - - +
117H SER* 3.0 16.4 + - - -
334H PRO* 3.5 23.5 - - + +
335H PHE* 3.7 25.6 - - + -
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Residues in contact with LEU 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H GLN 3.8 22.0 - - - +
14H GLN* 4.0 16.6 - - - +
15H PRO* 3.9 29.2 - - + +
41H ASN* 3.3 56.9 - - - +
42H PRO* 3.6 1.7 - - - +
48H ILE* 3.8 33.9 - - + -
104H ALA 2.8 20.0 + - - +
105H LEU* 3.6 14.6 - - + +
107H THR* 1.3 75.2 - - - +
109H ASP* 1.3 58.3 + - - +
335H PHE* 4.3 9.4 - - + -
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Residues in contact with ASP 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H THR* 2.7 12.4 + - - -
42H PRO* 3.5 7.1 - - - +
48H ILE* 3.4 13.8 - - + +
105H LEU* 3.1 14.9 + - + +
106H GLU* 4.2 2.5 - - - +
108H LEU* 1.3 80.3 - - + +
110H ASN* 1.3 58.2 + - + +
196H GLN 3.5 6.3 - - - +
197H THR* 3.3 23.0 - - + +
198H PRO* 3.4 10.6 - - - +
199H LEU* 3.5 30.3 + - + +
200H THR* 5.0 2.2 + - + +
345H VAL* 5.1 1.7 - - - +
3708H NA 2.4 50.1 - - - -
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Residues in contact with ASN 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H PRO* 3.4 12.4 - - - +
106H GLU* 2.8 22.5 + - + +
109H ASP* 1.3 74.5 - - + +
111H GLY* 1.3 55.8 + - - +
112H LYS* 2.8 47.1 + - - +
168H TRP* 3.0 25.1 + - - -
169H ASN* 3.4 16.6 + - - +
171H PRO* 4.1 8.4 - - + +
197H THR* 3.9 15.6 - - + +
297H ASN* 4.5 1.6 + - - +
298H GLN* 4.6 2.4 + - - -
300H GLN* 4.8 7.9 + - - +
343H PRO 4.5 2.8 - - - +
345H VAL* 4.0 22.0 + - - +
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Residues in contact with GLY 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H PRO* 3.7 13.9 - - - +
43H SER* 4.6 3.4 - - - -
107H THR 2.9 15.8 + - - -
110H ASN* 1.3 77.9 - - - +
112H LYS* 1.3 67.0 + - - +
298H GLN* 4.6 0.2 - - - -
334H PRO* 3.3 9.8 - - - +
342H GLY* 3.5 4.7 - - - -
343H PRO* 3.3 33.0 - - - +
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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