Contacts of the helix formed by residues 98 - 111 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94I LEU 3.0 9.6 + - - +
95I ILE 3.3 5.2 - - - +
96I GLU 3.2 0.2 - - - -
97I ARG* 1.3 115.7 + - - +
99I ARG* 1.3 56.2 - - - +
100I THR 3.4 2.2 - - - -
101I TYR* 3.4 7.1 + - + -
102I LEU* 2.9 33.9 + - + +
203I TYR* 2.6 41.5 + - + -
207I LEU* 3.6 3.7 - - + +
3127I EDO 4.2 19.6 + - - -
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Residues in contact with ARG 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95I ILE 3.0 9.2 + - - +
96I GLU* 3.2 28.4 + - - +
97I ARG 3.3 1.8 + - - -
98I ASP* 1.3 75.9 - - - +
100I THR* 1.3 58.4 + - - +
102I LEU* 3.4 0.7 + - - +
103I ALA* 2.9 33.3 + - - +
118I TYR* 2.7 70.2 + - + +
119I LEU* 4.0 7.7 + - - +
122I LEU* 3.9 23.9 - - + +
123I ASP* 3.8 29.6 + - - +
126I LEU* 4.5 18.7 - - - +
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Residues in contact with THR 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I PRO* 3.9 21.4 - - + +
10I ALA 3.9 17.0 - - - +
11I PRO* 4.7 3.6 - - + -
12I ASN 5.5 1.3 - - - +
97I ARG 5.1 1.2 + - - -
98I ASP 3.4 0.4 - - - -
99I ARG* 1.3 78.1 - - - +
101I TYR* 1.3 65.3 + - - +
103I ALA 3.5 0.2 + - - -
104I ALA* 3.2 21.3 + - - +
114I TYR* 3.4 24.0 - - + +
118I TYR* 3.9 14.1 + - - -
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Residues in contact with TYR 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I ASN* 6.1 4.3 - - + -
15I PRO* 3.9 19.7 - - + -
16I GLU 2.7 32.3 + - - -
17I VAL* 4.2 0.3 - - - -
18I PHE* 3.4 29.2 + + - -
98I ASP* 3.4 6.8 + - - +
99I ARG 3.4 0.4 - - - -
100I THR* 1.3 79.7 - - - +
102I LEU* 1.3 62.8 + - + +
104I ALA* 3.2 7.5 + - - +
105I LEU* 2.9 49.3 + - + +
203I TYR* 3.7 39.8 - + - -
3127I EDO 3.5 32.3 - - - +
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Residues in contact with LEU 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95I ILE* 4.1 34.1 - - + +
98I ASP* 2.9 23.5 + - + +
99I ARG 3.9 2.5 - - - +
101I TYR* 1.3 78.8 - - + +
103I ALA* 1.3 58.0 + - - +
105I LEU* 3.4 4.4 + - + +
106I GLU* 2.9 29.8 + - - +
122I LEU* 4.1 14.1 - - + -
172I LEU* 4.2 9.2 - - + +
200I THR* 4.0 33.4 - - + +
203I TYR* 3.8 34.8 - - + -
204I VAL* 4.4 11.2 - - + -
207I LEU* 4.5 3.4 - - + -
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Residues in contact with ALA 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99I ARG 2.9 17.9 + - - +
100I THR 3.9 0.2 - - - +
102I LEU* 1.3 75.8 - - - +
104I ALA* 1.3 61.2 + - - +
106I GLU* 3.4 1.3 + - - +
107I THR* 3.1 26.7 + - - -
114I TYR* 3.7 20.6 - - + -
117I SER* 3.4 6.9 - - - -
118I TYR* 3.7 34.1 - - + +
122I LEU* 3.8 13.1 - - + +
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Residues in contact with ALA 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I ASN* 3.5 31.9 - - + +
15I PRO* 4.2 9.2 - - + -
100I THR 3.2 13.7 + - - +
101I TYR* 3.2 9.8 + - - +
103I ALA* 1.3 75.1 - - - +
105I LEU* 1.3 60.3 + - - +
107I THR 3.3 1.2 + - - -
108I LEU* 2.8 26.9 + - - +
114I TYR* 3.7 13.4 - - + -
335I PHE* 3.4 17.7 - - + -
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Residues in contact with LEU 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I PRO* 4.0 20.1 - - + +
16I GLU 4.5 5.2 - - - +
17I VAL* 4.3 16.2 - - + -
101I TYR* 2.9 42.0 + - + +
102I LEU* 3.7 6.7 - - + +
104I ALA* 1.3 73.5 - - - +
106I GLU* 1.3 66.2 + - - +
108I LEU* 3.8 5.8 - - + +
109I ASP* 3.1 24.3 + - - +
199I LEU* 4.0 31.6 - - + +
200I THR* 3.7 30.9 - - + +
203I TYR* 4.5 6.1 - - + -
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Residues in contact with GLU 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I LEU 2.9 17.6 + - - +
103I ALA* 3.5 7.6 - - - +
104I ALA 3.2 0.2 - - - -
105I LEU* 1.3 75.7 - - - +
107I THR* 1.3 54.2 + - - +
109I ASP* 4.0 1.4 - - - +
110I ASN* 2.8 41.3 + - + +
112I LYS* 4.2 14.6 - - + -
117I SER* 3.9 13.5 - - - +
121I ASP* 4.2 12.4 - - + +
122I LEU* 5.2 0.2 - - + -
171I PRO* 3.3 26.7 - - + +
172I LEU* 3.0 39.5 + - + +
173I LEU 4.6 0.3 + - - -
197I THR* 5.6 0.2 - - - -
200I THR* 2.8 29.2 + - + +
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Residues in contact with THR 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I ASN* 5.0 0.9 - - - +
43I SER* 5.2 0.2 + - - -
103I ALA 3.1 4.5 + - - -
104I ALA 3.5 6.3 - - - -
106I GLU* 1.3 78.8 - - - +
108I LEU* 1.3 58.6 + - - +
111I GLY* 2.8 28.0 + - - +
112I LYS 2.8 28.7 + - - +
114I TYR* 3.1 19.5 - - - +
117I SER* 2.9 17.7 + - - -
334I PRO* 3.6 26.1 - - + +
335I PHE* 3.7 23.8 - - + -
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Residues in contact with LEU 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I GLN 3.7 23.3 - - - +
14I GLN* 4.9 4.5 - - + -
15I PRO* 4.0 28.9 - - + +
41I ASN* 3.2 60.6 - - - +
42I PRO* 3.6 0.9 - - - +
48I ILE* 3.6 32.7 - - + +
104I ALA 2.8 20.1 + - - +
105I LEU* 3.3 12.7 + - + +
107I THR* 1.3 73.2 - - - +
109I ASP* 1.3 58.4 + - - +
334I PRO* 6.2 0.2 - - - -
335I PHE* 4.3 9.6 - - + -
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Residues in contact with ASP 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I THR* 2.8 13.9 + - - +
42I PRO* 3.5 7.7 - - - +
48I ILE* 3.5 12.9 - - + +
105I LEU 3.1 16.7 + - - +
106I GLU* 4.1 2.2 - - - +
108I LEU* 1.3 77.4 - - + +
110I ASN* 1.3 60.2 + - - +
196I GLN 3.5 6.8 - - - +
197I THR* 3.2 24.1 - - + +
198I PRO* 3.4 2.6 - - - +
199I LEU* 3.4 36.7 + - + +
200I THR* 4.8 3.2 + - + -
345I VAL* 5.0 1.9 - - - +
3709I NA 2.5 45.9 - - - -
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Residues in contact with ASN 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I PRO* 3.5 11.9 - - - +
106I GLU* 2.8 19.1 + - - +
109I ASP* 1.3 80.1 - - - +
111I GLY* 1.3 54.5 + - - +
112I LYS* 2.9 37.7 + - - +
168I TRP* 2.8 28.9 + - - -
169I ASN* 3.7 13.5 + - - +
171I PRO* 4.0 8.7 - - + +
197I THR* 3.7 14.8 - - + +
297I ASN* 4.5 1.4 + - - +
298I GLN* 4.7 3.1 + - - -
300I GLN* 4.8 7.2 + - - +
343I PRO 4.7 2.4 - - - +
345I VAL* 4.0 20.7 + - - +
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Residues in contact with GLY 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I PRO* 3.7 15.3 - - - +
43I SER* 4.7 3.6 - - - -
107I THR 2.8 21.6 + - - -
110I ASN* 1.3 73.1 - - - +
112I LYS* 1.3 67.1 + - - +
298I GLN* 4.5 4.0 - - - -
334I PRO* 3.3 15.3 - - - +
342I GLY* 3.5 4.5 - - - -
343I PRO* 3.4 22.5 - - - +
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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