Contacts of the helix formed by residues 49 - 60 (chain B) in PDB entry 1ZB8
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 ASN 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A TYR* 2.9 41.4 + - - -
19B ARG* 4.9 1.6 - - + +
34B LEU* 4.0 4.5 - - + -
35B SER 3.9 11.1 + - - +
37B PRO* 3.9 14.1 - - + +
47B GLY 4.6 2.6 + - - -
48B THR* 1.3 82.8 + - - +
50B PRO* 1.4 79.1 - - + +
51B GLU* 3.2 7.7 + - - +
52B GLN* 2.9 40.7 + - - +
53B LEU* 3.0 28.2 + - - +
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Residues in contact with PRO 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLY* 3.3 36.8 - - - +
60A ALA* 4.2 0.2 - - + -
61A OCS 4.2 7.2 - - - +
127A TYR* 3.0 22.9 + - + +
19B ARG* 3.4 40.2 - - + +
34B LEU* 3.8 16.3 - - + -
49B ASN* 1.4 90.0 - - + +
51B GLU* 1.3 60.7 + - - +
53B LEU* 3.7 1.7 - - + +
54B PHE* 2.8 27.2 + - - +
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 4.1 5.1 - - + -
11A ALA* 3.3 16.7 - - + +
127A TYR* 2.9 24.6 + - - +
19B ARG* 2.6 46.8 + - - -
40B LEU* 4.3 2.9 - - - +
49B ASN* 3.1 12.3 - - - +
50B PRO* 1.3 75.1 - - - +
52B GLN* 1.3 60.1 + - - +
54B PHE* 3.5 0.4 + - - -
55B ALA* 2.8 30.3 + - - +
87B VAL* 3.5 26.7 - - + +
89B ILE* 3.6 34.2 - - + +
98B LEU* 3.7 1.0 - - + +
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Residues in contact with GLN 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 3.3 24.8 + - - +
11A ALA* 3.3 12.7 - - + +
12A ILE 4.9 2.6 + - - +
13A VAL* 3.5 12.3 - - + +
25A SER* 3.6 16.3 + - - -
26A SER* 5.2 1.0 + - - +
27A ASP* 2.9 38.0 + - - -
29A VAL* 3.1 15.8 - - - +
30A LEU* 3.7 6.4 - - + +
48B THR* 2.7 33.8 + - - +
49B ASN* 2.9 16.0 + - - +
51B GLU* 1.3 75.3 - - - +
53B LEU* 1.3 57.9 + - - +
55B ALA* 3.5 1.6 - - - +
56B ALA* 2.9 31.7 + - - +
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 3.9 22.2 - - + -
53A LEU* 3.2 52.3 - - + +
56A ALA* 4.0 7.0 - - + -
57A GLY* 3.9 17.5 - - - +
30B LEU* 4.2 15.9 - - + -
32B VAL* 4.3 4.0 - - + -
34B LEU* 4.1 13.9 - - + -
48B THR* 3.9 19.5 - - + +
49B ASN 3.0 30.0 + - - +
50B PRO* 3.8 4.9 - - + +
52B GLN* 1.3 76.2 - - - +
54B PHE* 1.3 61.2 + - - +
56B ALA* 3.5 1.0 - - - +
57B GLY 3.2 17.3 + - - -
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Residues in contact with PHE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU 4.3 2.1 + - - -
54A PHE* 3.4 34.5 - + + +
57A GLY* 5.2 0.6 - - - -
127A TYR* 3.7 28.0 - + + +
130A ALA* 5.6 0.9 - - + -
50B PRO 2.8 17.8 + - - +
51B GLU 3.8 2.2 - - - +
53B LEU* 1.3 73.5 - - - +
55B ALA* 1.3 64.8 + - - +
57B GLY* 3.2 1.4 + - - -
58B TYR* 3.0 52.6 + + + +
87B VAL* 3.7 19.3 - - + -
98B LEU* 4.2 13.2 - - + -
100B VAL* 3.7 19.1 - - + -
127B TYR* 4.1 14.6 - + + -
131B THR* 3.9 22.0 - - + -
135B ILE* 4.5 4.0 - - + -
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA* 4.4 2.7 - - + -
13A VAL* 3.4 21.9 - - + +
51B GLU 2.8 21.9 + - - +
52B GLN* 3.3 6.0 + - - +
54B PHE* 1.3 72.4 - - - +
56B ALA* 1.3 51.9 + - - +
58B TYR* 3.9 2.8 - - - +
59B SER* 2.7 40.4 + - - -
85B GLY* 3.8 17.1 - - - +
86B ARG 5.1 0.2 - - - +
87B VAL* 3.5 21.4 - - + +
100B VAL* 6.2 0.2 - - - -
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 3.4 11.4 - - + +
23A VAL* 3.4 24.4 - - + +
30A LEU* 3.7 16.2 - - + -
32A VAL* 5.2 0.2 - - + -
53A LEU* 3.8 15.5 - - + -
52B GLN 2.9 18.0 + - - +
53B LEU 3.5 6.3 - - - +
54B PHE 3.2 0.2 - - - -
55B ALA* 1.3 73.7 - - - +
57B GLY* 1.3 65.1 + - - +
60B ALA* 3.1 27.2 + - - +
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Residues in contact with GLY 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PRO* 3.2 42.7 - - - +
53A LEU* 3.9 5.8 - - - +
54A PHE* 5.4 0.7 - - - -
53B LEU 3.2 10.2 + - - -
54B PHE* 3.2 2.0 + - - -
56B ALA* 1.3 77.5 - - - +
58B TYR* 1.3 65.0 + - - +
61B OCS 3.0 21.0 + - - +
127B TYR* 4.9 3.8 - - - -
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Residues in contact with TYR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B PHE* 3.0 45.6 + + + +
55B ALA* 3.9 4.0 - - - +
57B GLY* 1.3 74.6 - - - +
59B SER* 1.3 52.1 + - - +
61B OCS 3.3 3.3 + - - +
62B PHE* 2.7 32.8 + + + +
100B VAL* 3.7 31.0 - - + -
102B LEU* 3.7 28.5 - - + -
122B HIS* 3.8 0.2 - - - -
125B CYS* 3.6 15.9 - - - -
127B TYR* 3.7 28.2 - - + -
128B SER* 2.5 43.5 + - - -
131B THR* 4.2 3.8 - - - -
137B VAL* 3.5 16.5 - - + +
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Residues in contact with SER 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 3.5 14.4 - - - +
15A ALA* 3.5 15.4 + - - +
55B ALA 2.7 23.4 + - - -
56B ALA 3.5 1.9 + - - -
58B TYR* 1.3 75.6 - - - +
60B ALA* 1.3 63.0 + - - +
62B PHE* 3.4 0.6 + - - -
63B ILE* 3.2 27.2 + - - +
83B VAL* 3.6 30.1 - - - +
85B GLY* 3.8 18.6 - - - -
102B LEU* 4.2 4.0 - - - -
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Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA* 3.7 9.0 - - + -
18A GLY* 3.1 33.9 - - - +
19A ARG 3.9 1.0 + - - -
23A VAL* 3.8 9.2 - - + -
34A LEU* 3.6 29.6 - - + -
50A PRO* 4.3 1.3 - - + -
56B ALA 3.1 20.0 + - - +
57B GLY 3.8 2.9 - - - +
59B SER* 1.3 74.2 + - - +
61B OCS 1.3 66.6 + - - +
63B ILE* 3.4 8.0 + - - +
64B GLY 3.6 1.6 + - - -
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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