Contacts of the strand formed by residues 28 - 36 (chain A) in PDB entry 4AG1
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 LYS 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLU* 3.6 4.5 - - - +
20A ILE* 2.8 56.5 + - + +
22A THR* 4.2 16.7 - - + +
26A PRO 4.0 0.4 + - - -
27A SER* 1.3 75.8 - - - +
29A PHE* 1.3 65.3 + - - +
30A CYS* 5.7 2.2 - - - -
45A HIS 2.9 25.9 + - - -
46A CYS* 3.7 9.1 - - - +
47A ALA 2.9 25.4 + - - -
39C GLU* 2.7 30.4 + - - +
48C THR* 4.5 13.7 - - + -
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Residues in contact with PHE 29 (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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17A TYR* 3.4 41.1 - + + +
18A LEU 3.1 13.5 - - - +
19A GLU* 4.8 1.8 - - + -
20A ILE* 4.1 1.3 - - - -
28A LYS* 1.3 79.4 - - - +
30A CYS* 1.3 75.6 + - - +
128A TRP* 3.6 28.9 - - + -
129A GLY* 4.3 2.2 - - - -
130A ARG* 5.3 0.7 - - + -
137A GLY* 4.5 13.2 - - - -
179A LYS 5.1 0.4 - - - -
180A GLY* 3.5 40.3 - - - -
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Residues in contact with CYS 30 (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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17A TYR* 3.8 4.7 - - - -
18A LEU* 2.9 32.9 + - + +
20A ILE* 4.1 8.5 - - + +
28A LYS* 5.7 3.1 - - - -
29A PHE* 1.3 88.2 - - - +
31A GLY* 1.3 65.4 + - - +
42A THR* 4.4 0.2 - - - +
45A HIS* 4.9 3.8 - - - -
46A CYS* 2.0 56.1 - - + -
128A TRP* 5.9 0.4 - - - -
180A GLY* 3.9 10.1 - - - -
182A SER* 3.5 12.8 - - - +
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Residues in contact with GLY 31 (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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15A MET* 5.1 5.2 - - - -
16A ALA 3.4 9.9 - - - -
17A TYR* 5.0 0.4 - - - -
18A LEU* 3.7 4.9 - - - +
30A CYS* 1.3 77.0 - - - +
32A GLY* 1.3 51.4 + - - -
42A THR* 2.7 28.4 + - - -
128A TRP* 5.1 6.1 - - - -
180A GLY 3.7 7.5 + - - -
181A ASP* 4.7 2.2 - - - -
182A SER 2.8 17.8 + - - +
183A GLY* 3.4 4.1 - - - -
184A GLY* 4.2 7.0 - - - -
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Residues in contact with GLY 32 (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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15A MET* 3.8 10.6 - - - +
16A ALA* 2.9 29.1 + - - -
18A LEU* 4.2 7.0 - - - -
31A GLY* 1.3 74.3 - - - -
33A PHE* 1.3 67.0 + - - +
40A VAL* 4.3 0.9 - - - -
41A LEU 3.2 14.6 - - - -
42A THR* 4.2 2.9 - - - -
183A GLY 3.3 10.3 + - - -
184A GLY* 4.1 1.2 - - - +
185A PRO* 4.6 0.4 - - - -
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Residues in contact with PHE 33 (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 TYR* 3.2 19.1 - - + +
16A ALA 4.3 0.9 - - - +
32A GLY* 1.3 75.6 - - - +
34A LEU* 1.3 62.8 + - - +
35A ILE* 3.5 15.1 + - + +
40A VAL* 3.3 8.0 - - - +
41A LEU* 2.9 72.5 + - + -
108A LEU* 3.6 25.4 - - + -
110A PHE* 4.4 0.9 - + - -
183A GLY 3.5 22.7 - - - -
185A PRO* 3.5 36.3 - - + -
192A ALA* 4.3 8.7 - - + -
195A ILE* 3.9 19.3 - - + -
212A ILE* 4.0 6.1 - - + -
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Residues in contact with LEU 34 (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 TYR* 2.9 13.7 + - - +
16A ALA* 4.8 0.8 - - - +
33A PHE* 1.3 71.0 - - - +
35A ILE* 1.3 61.0 + - - +
36A ARG 3.1 25.4 - - - +
37A ARG 4.0 10.1 - - - +
39A PHE 3.5 8.3 - - - +
40A VAL* 3.8 16.0 - - + +
55A LEU* 4.1 20.9 - - + -
95A LEU* 4.2 3.6 - - + -
99A ALA* 4.2 9.4 - - + -
101A LEU* 4.4 4.9 - - + -
105A VAL* 4.1 21.1 - - + -
106A GLY* 3.6 30.7 - - - +
107A THR* 3.3 9.2 - - + -
108A LEU* 2.9 27.5 + - - +
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Residues in contact with ILE 35 (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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33A PHE* 3.5 24.9 + - + +
34A LEU* 1.3 78.1 - - - +
36A ARG* 1.3 88.6 + - + +
39A PHE* 2.9 21.2 + - + +
41A LEU* 4.2 10.8 - - + +
92A LEU* 3.7 26.0 - - + -
107A THR* 3.7 15.3 - - - +
108A LEU 4.5 5.7 - - - +
110A PHE* 3.5 35.0 - - + -
219A ILE* 4.0 19.5 - - + -
223A LEU* 4.2 13.7 - - + -
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Residues in contact with ARG 36 (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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34A LEU* 3.1 13.7 - - - +
35A ILE* 1.3 96.8 + - + +
37A ARG* 1.3 68.4 + - - +
38A ASN* 3.0 9.0 + - - +
39A PHE* 3.1 24.2 + - + +
107A THR* 3.8 10.5 - - - -
110A PHE* 5.7 5.7 - - - -
220A ASN* 5.0 6.1 + - - -
223A LEU* 3.7 44.4 - - + +
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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