Contacts of the helix formed by residues 11 - 19 (chain B) in PDB entry 1Z5A
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 SER 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LEU* 4.4 0.9 - - - -
10B LEU* 1.3 76.2 - - - +
12B PRO* 1.3 75.5 - - - +
13B ALA 3.3 4.0 + - - -
14B GLU* 3.0 15.1 + - - -
15B PHE* 3.0 21.0 + - - +
148B ILE 2.6 24.7 + - - -
149B ASN 3.5 21.1 - - - -
150B LYS 4.8 0.7 - - - -
151B ASN* 3.8 9.6 - - - +
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Residues in contact with PRO 12 (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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10A LEU 5.6 1.1 - - - +
12A PRO* 4.1 22.0 - - + -
94A LEU* 4.3 6.5 - - + -
10B LEU 4.5 1.3 - - - +
11B SER* 1.3 89.3 - - - +
13B ALA* 1.3 60.2 + - - +
15B PHE* 3.5 7.7 + - + +
16B PHE* 3.2 33.7 + - + -
93B VAL* 3.8 22.9 - - + +
94B LEU* 3.9 25.8 - - + -
151B ASN* 4.0 16.8 - - + +
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Residues in contact with ALA 13 (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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11B SER* 3.1 2.2 + - - -
12B PRO* 1.3 76.2 - - - +
14B GLU* 1.3 61.4 + - - +
16B PHE* 3.3 2.3 + - - -
17B LYS* 2.9 31.3 + - - +
93B VAL* 3.8 15.9 - - + -
117B LEU* 3.9 13.2 - - + +
146B ILE* 4.4 4.0 - - + -
148B ILE* 3.6 29.8 - - + +
151B ASN* 3.4 22.3 + - - +
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ILE* 6.0 2.2 - - + +
9B SER 4.3 2.3 - - - +
10B LEU* 3.5 25.7 - - + +
11B SER* 3.0 28.3 + - - +
13B ALA* 1.3 78.2 - - - +
15B PHE* 1.3 57.7 + - - +
17B LYS* 3.3 6.4 + - - +
18B ARG* 2.9 38.5 + - - +
148B ILE* 3.5 31.9 - - + +
149B ASN* 3.0 39.4 + - - +
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Residues in contact with PHE 15 (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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16A PHE* 4.7 19.1 - + - -
94A LEU* 3.6 35.4 - - + -
108A TYR* 3.6 42.6 - + + -
110A LEU* 5.5 1.3 - - + -
425A ALA* 5.1 4.3 - - + -
10B LEU* 4.1 16.7 - - + +
11B SER 3.0 11.8 + - - +
12B PRO* 3.6 9.4 - - + +
14B GLU* 1.3 77.8 - - - +
16B PHE* 1.3 86.9 + + - +
18B ARG* 4.8 0.2 - - - -
19B ASN* 2.9 39.6 + - - +
22B LEU* 3.7 29.8 - - + -
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Residues in contact with PHE 16 (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 PHE* 4.6 20.0 - + - -
16A PHE* 5.7 0.2 - + - -
12B PRO* 3.2 23.9 + - + +
13B ALA 3.3 3.0 + - - -
15B PHE* 1.3 104.2 - + - +
17B LYS* 1.3 63.8 + - - +
19B ASN 4.2 3.1 - - - +
20B PRO* 3.0 28.3 - - + +
22B LEU* 4.2 25.8 - - + -
23B ALA* 4.4 9.6 - - + -
93B VAL* 4.1 9.9 - - + -
94B LEU* 4.9 8.3 - - + -
110B LEU* 3.9 43.5 - - + -
114B ALA* 5.8 0.9 - - + -
117B LEU* 4.0 20.8 - - + +
121B MET* 5.1 0.3 - - - +
425B ALA* 4.8 4.9 - - + -
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Residues in contact with LYS 17 (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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237A ASP* 2.6 34.1 + - - -
239A GLU* 3.9 12.8 - - + -
240A GLU* 3.5 32.3 + - - +
243A ILE* 4.6 7.2 - - + -
13B ALA 2.9 17.7 + - - +
14B GLU* 3.7 7.0 - - - +
16B PHE* 1.3 75.8 - - - +
18B ARG* 1.3 76.2 + - + +
20B PRO* 3.3 10.7 - - - +
117B LEU* 4.2 12.2 - - + +
121B MET* 3.4 31.2 - - + +
148B ILE* 4.1 25.6 - - + -
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Residues in contact with ARG 18 (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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98A LYS 4.6 2.4 + - - -
99A TYR* 3.3 49.1 + - - +
100A VAL 5.2 2.2 + - - -
107A MET 5.0 3.8 + - - -
240A GLU* 5.9 1.8 - - - +
348A HIS* 5.5 2.7 + - - -
419A LYS* 2.8 26.9 + - - +
10B LEU* 3.9 33.9 - - - +
14B GLU* 2.9 21.6 + - - +
17B LYS* 1.3 91.6 - - + +
19B ASN* 1.3 74.7 + - - +
20B PRO* 3.3 1.4 - - - +
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Residues in contact with ASN 19 (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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107A MET* 3.7 25.3 + - - +
108A TYR* 3.7 22.6 + - + -
419A LYS* 4.2 6.6 - - - +
10B LEU* 5.7 0.4 - - - +
15B PHE* 2.9 35.6 + - - +
16B PHE* 3.2 9.6 + - - +
18B ARG* 1.3 95.0 + - - +
20B PRO* 1.3 64.8 - - - +
21B GLU* 3.1 14.1 - - - +
22B LEU* 3.0 36.1 + - + +
23B ALA 4.3 0.5 + - - -
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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