Contacts of the helix formed by residues 98 - 111 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94K LEU 3.1 8.4 + - - +
95K ILE 3.3 5.2 - - - +
96K GLU 3.2 0.2 - - - -
97K ARG* 1.3 116.1 + - - +
99K ARG* 1.3 56.3 + - - -
100K THR 3.5 2.0 - - - -
101K TYR* 3.4 12.2 + - + -
102K LEU* 2.9 33.2 + - + +
203K TYR* 2.8 37.7 + - + +
207K LEU* 3.3 11.7 - - + +
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Residues in contact with ARG 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K ILE* 2.9 10.5 + - + +
96K GLU* 3.2 32.0 + - - +
97K ARG 3.3 1.8 + - - -
98K ASP* 1.3 75.0 - - - +
100K THR* 1.3 65.0 + - - +
102K LEU 3.2 0.5 + - - -
103K ALA* 2.9 23.0 + - - +
118K TYR* 2.9 65.8 + - + +
119K LEU* 4.0 10.3 + - - +
122K LEU* 3.0 32.6 - - + +
123K ASP* 3.7 28.7 + - - +
126K LEU* 4.5 15.0 - - + +
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Residues in contact with THR 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K PRO* 3.8 24.6 - - + +
10K ALA 4.0 16.8 - - - +
11K PRO* 4.7 3.6 - - + -
12K ASN 5.4 2.2 - - - +
97K ARG 5.2 0.8 + - - -
98K ASP 3.5 0.2 - - - -
99K ARG* 1.3 77.8 - - - +
101K TYR* 1.3 64.3 + - - +
103K ALA* 3.3 2.8 + - - +
104K ALA* 3.1 22.4 + - - +
114K TYR* 3.6 19.6 - - + +
118K TYR* 3.9 12.0 + - - -
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Residues in contact with TYR 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K ASN* 6.4 1.1 - - + -
15K PRO* 4.0 19.0 - - + +
16K GLU 2.7 32.3 + - - -
17K VAL* 4.2 2.8 - - - -
18K PHE* 3.5 25.6 + + - -
98K ASP* 3.4 13.6 + - + +
99K ARG 3.3 0.4 - - - -
100K THR* 1.3 79.7 - - - +
102K LEU* 1.3 64.2 + - + +
104K ALA* 3.2 8.2 + - - +
105K LEU* 3.0 51.5 + - + +
203K TYR* 3.8 45.5 - + - +
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Residues in contact with LEU 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K ILE* 4.0 28.0 - - + +
98K ASP* 2.9 24.3 + - + +
101K TYR* 1.3 78.0 - - + +
103K ALA* 1.3 61.0 + - - +
105K LEU* 3.8 4.0 - - + +
106K GLU* 2.9 30.1 + - - +
122K LEU* 3.8 12.8 - - + -
172K LEU* 4.2 11.2 - - + +
200K THR* 4.0 33.2 - - + +
203K TYR* 3.7 28.0 - - + -
204K VAL* 4.4 8.1 - - + -
207K LEU* 4.3 19.5 - - + -
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Residues in contact with ALA 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K ARG 2.9 16.6 + - - +
100K THR 3.7 0.4 - - - +
102K LEU* 1.3 76.0 - - - +
104K ALA* 1.3 62.8 + - - +
106K GLU* 3.3 5.8 + - - +
107K THR* 3.1 26.7 + - - -
114K TYR* 3.6 21.5 - - + -
117K SER* 3.4 7.3 - - - -
118K TYR* 3.8 32.8 - - + +
122K LEU* 3.6 8.9 - - + +
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Residues in contact with ALA 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K ASN* 3.6 31.2 - - + +
15K PRO* 4.1 8.5 - - + -
100K THR* 3.1 10.3 + - + +
101K TYR* 3.5 10.3 - - - +
103K ALA* 1.3 77.4 - - - +
105K LEU* 1.3 60.1 + - - +
107K THR* 3.3 3.6 + - - -
108K LEU* 2.9 25.3 + - - +
114K TYR* 3.8 15.0 - - + -
335K PHE* 3.6 15.6 - - + -
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Residues in contact with LEU 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K PRO* 3.9 21.0 - - + +
17K VAL* 4.1 17.0 - - + -
101K TYR* 3.0 46.5 + - + +
102K LEU* 3.8 7.2 - - + +
104K ALA* 1.3 74.4 - - - +
106K GLU* 1.3 65.1 + - - +
108K LEU* 3.3 7.3 + - + +
109K ASP* 3.1 24.4 + - - +
199K LEU* 3.9 35.2 - - + +
200K THR* 4.0 29.2 - - + +
203K TYR* 4.6 5.2 - - + -
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Residues in contact with GLU 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102K LEU 2.9 19.0 + - - +
103K ALA* 3.3 8.5 - - - +
105K LEU* 1.3 76.3 - - - +
107K THR* 1.3 52.4 - - - +
109K ASP* 3.9 2.1 - - - +
110K ASN* 2.7 40.9 + - + +
112K LYS* 4.4 12.1 - - + -
117K SER* 3.6 16.2 - - - +
121K ASP* 4.3 12.1 - - + +
122K LEU* 5.1 0.4 - - + -
171K PRO* 3.3 25.3 - - - +
172K LEU* 3.0 41.4 + - + +
173K LEU 4.7 0.2 + - - -
197K THR* 5.5 0.3 - - - -
200K THR* 3.1 22.4 + - + +
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Residues in contact with THR 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43K SER* 5.2 1.0 + - - -
103K ALA 3.1 5.9 + - - -
104K ALA 3.5 7.2 - - - -
106K GLU* 1.3 79.5 - - - +
108K LEU* 1.3 59.7 + - - +
111K GLY* 2.8 28.2 + - - +
112K LYS 2.9 27.7 + - - +
114K TYR* 3.1 22.5 - - - +
117K SER* 3.2 8.8 + - - -
334K PRO* 3.6 24.6 - - + +
335K PHE* 3.7 26.5 - - + -
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Residues in contact with LEU 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K GLN 3.4 25.6 - - - +
14K GLN* 4.7 5.8 - - + -
15K PRO* 3.9 28.7 - - + +
41K ASN* 3.4 53.8 - - - +
42K PRO* 3.7 0.9 - - - +
48K ILE* 3.6 30.0 - - + +
104K ALA 2.9 16.9 + - - +
105K LEU* 3.3 11.6 + - + +
107K THR* 1.3 76.7 - - - +
109K ASP* 1.3 61.2 + - - +
335K PHE* 4.0 9.6 - - + -
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Residues in contact with ASP 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K THR* 2.7 15.4 + - - -
42K PRO* 3.5 6.7 - - - +
48K ILE* 3.4 12.2 - - + +
105K LEU 3.1 16.0 + - - +
106K GLU* 4.2 2.9 - - - +
108K LEU* 1.3 79.6 - - - +
110K ASN* 1.3 57.8 + - - +
196K GLN 3.5 7.6 - - - +
197K THR* 3.2 24.4 - - + +
198K PRO* 3.3 12.1 - - - +
199K LEU* 3.3 27.4 + - + +
200K THR* 5.0 2.4 + - + +
345K VAL* 5.1 1.2 - - - +
3711K NA 2.4 47.3 - - - -
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Residues in contact with ASN 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K PRO* 3.3 13.0 - - - +
106K GLU* 2.7 23.7 + - - +
109K ASP* 1.3 75.4 - - - +
111K GLY* 1.3 55.0 + - - +
112K LYS* 3.0 46.9 + - - +
168K TRP* 2.8 34.1 + - - -
169K ASN* 3.5 12.3 + - - +
171K PRO* 4.1 8.0 - - + +
197K THR* 3.8 12.6 - - + +
297K ASN* 4.3 2.1 - - - +
298K GLN* 4.5 2.4 + - - -
300K GLN* 5.1 7.6 + - - +
343K PRO 4.7 2.3 - - - +
345K VAL* 4.1 15.4 + - - +
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Residues in contact with GLY 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K PRO* 3.8 12.8 - - - +
43K SER* 4.6 3.8 - - - -
107K THR 2.8 21.4 + - - -
110K ASN* 1.3 73.4 - - - +
112K LYS* 1.3 65.7 + - - +
298K GLN* 4.7 3.1 - - - -
334K PRO* 3.2 16.0 - - - +
342K GLY* 3.6 4.1 - - - -
343K PRO* 3.5 24.2 - - - +
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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