Contacts of the strand formed by residues 9 - 18 (chain A) in PDB entry 4ZCH
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 VAL 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A HIS 3.8 1.3 - - - +
8A SER* 1.3 76.3 - - - +
10A LEU* 1.3 66.4 + - - +
34A LEU* 4.8 4.0 - - + +
35A ARG* 3.5 5.9 - - - +
36A ARG* 3.0 67.2 + - + +
40A LEU* 4.6 2.6 - - - +
139A PHE 3.4 10.1 - - - +
140A VAL* 5.0 6.5 - - + -
351A TYR* 3.7 33.2 - - + -
409A ILE* 4.3 18.4 - - + -
443A LEU* 4.6 13.5 - - + -
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 1.3 74.5 - - - +
11A HIS* 1.4 57.1 + - - +
12A LEU* 3.6 30.1 - - + -
32A PRO* 3.8 21.1 - - + -
34A LEU 3.2 16.4 - - - +
35A ARG* 3.7 27.8 - - + -
40A LEU* 3.8 31.4 - - + +
42A ALA 4.7 5.6 - - - +
47A VAL* 3.7 23.6 - - + -
137A LEU 3.9 0.4 - - - +
138A GLY* 3.1 5.2 - - - -
139A PHE* 2.9 37.4 + - + +
409A ILE* 4.1 3.5 - - - +
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Residues in contact with HIS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 5.3 0.2 - - - +
10A LEU* 1.4 71.7 - - - +
12A LEU* 1.3 54.7 + - - +
13A VAL* 4.3 8.0 - - + +
32A PRO* 3.7 1.6 - - - +
33A ALA* 2.7 46.8 + - + +
34A LEU* 2.8 37.8 + - + +
58A TYR* 2.7 30.0 + + - +
132A PRO 4.8 2.4 + - - -
136A PHE* 3.6 42.7 - + + +
137A LEU 3.5 3.0 + - - -
388A LEU 5.5 0.8 + - - -
389A PHE* 4.1 20.7 - + - -
409A ILE* 4.1 14.3 + - + +
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Residues in contact with LEU 12 (chain A).
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* 3.6 30.7 - - + -
11A HIS* 1.3 76.6 + - - +
13A VAL* 1.4 63.1 + - - +
30A TRP* 3.6 34.8 - - + -
31A GLN 3.4 14.4 - - - +
32A PRO* 4.2 2.5 - - + -
42A ALA* 3.8 26.2 - - + -
47A VAL* 3.8 10.1 - - + -
136A PHE* 3.3 10.9 - - - +
137A LEU* 2.7 45.9 + - + +
139A PHE* 3.7 21.8 - - + -
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Residues in contact with VAL 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A HIS* 4.3 9.6 - - - +
12A LEU* 1.4 78.2 - - - +
14A PRO* 1.4 73.9 - - + +
30A TRP* 3.6 4.0 - - - -
31A GLN* 2.9 58.9 + - + +
33A ALA* 4.1 23.6 - - + -
132A PRO* 3.7 41.1 - - + +
135A THR 4.5 0.9 - - - +
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Residues in contact with PRO 14 (chain A).
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* 1.4 91.0 - - + +
15A ILE* 1.3 60.9 + - - +
16A ASN 4.7 1.1 - - - +
28A VAL* 3.6 15.9 - - + -
29A MET 3.3 7.4 - - - +
30A TRP* 3.7 9.1 - - + -
31A GLN* 3.5 10.3 + - - -
130A LEU* 3.7 42.7 - - + +
131A SER 4.5 0.4 - - - +
135A THR* 3.1 48.0 - - + +
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Residues in contact with ILE 15 (chain A).
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 3.7 0.2 + - - -
14A PRO* 1.3 76.4 - - - +
16A ASN* 1.3 75.9 + - + +
29A MET* 2.7 49.6 + - + +
30A TRP 4.6 6.5 - - - +
31A GLN* 3.4 35.2 - - + +
130A LEU* 4.5 7.2 - - - +
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Residues in contact with ASN 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A PRO* 3.8 0.4 - - - +
15A ILE* 1.3 92.4 - - + +
17A ALA* 1.3 71.8 + - - +
18A ALA* 5.8 1.2 - - - +
28A VAL* 3.8 4.3 - - - +
29A MET* 2.8 45.4 + - + +
45A TYR* 5.3 4.3 - - - +
130A LEU* 4.0 12.4 - - - +
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Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ASN* 1.3 88.7 + - - +
18A ALA* 1.3 62.9 + - - +
26A THR* 4.2 15.5 - - + -
27A GLU 3.3 15.3 - - - +
28A VAL* 4.7 2.7 - - - -
45A TYR* 5.2 2.2 - - - -
126A ALA 6.0 0.7 - - - +
128A LEU* 4.9 7.0 - - + -
130A LEU* 4.1 23.5 - - + +
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ASN* 5.8 1.1 - - - +
17A ALA* 1.3 76.2 - - - +
19A SER* 1.3 64.9 + - - +
25A VAL 4.1 0.2 - - - +
26A THR* 3.5 3.6 - - - +
27A GLU* 3.0 33.9 + - - +
45A TYR* 4.6 17.3 - - + +
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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