Contacts of the strand formed by residues 25 - 32 (chain A) in PDB entry 1EAG
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 GLN 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A THR* 3.1 4.9 - - - -
20A VAL* 2.6 45.2 + - + +
23A ASN* 2.6 43.6 + - - +
24A ASN* 1.3 71.8 - - - +
26A LYS* 1.3 63.3 + - - +
27A LEU* 3.6 13.8 + - + +
64A THR 4.1 6.1 - - - +
65A TYR* 3.7 10.2 - - + -
66A ASP* 2.9 50.9 + - - +
70A SER* 3.9 7.7 - - - +
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Residues in contact with LYS 26 (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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18A ILE 3.7 5.6 - - - +
19A THR* 4.3 11.0 - - + -
24A ASN* 3.2 11.0 + - + +
25A GLN* 1.3 71.1 - - - +
27A LEU* 1.4 65.0 + - - +
62A LYS 4.3 0.3 - - - +
63A GLY* 3.8 13.0 - - - -
64A THR 4.7 1.7 + - - +
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Residues in contact with LEU 27 (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 ASP* 3.7 3.8 - - - +
18A ILE* 3.0 41.6 + - + +
20A VAL* 4.1 21.3 - - + -
25A GLN* 3.6 19.4 + - + +
26A LYS* 1.4 78.1 - - - +
28A ASN* 1.3 61.4 + - - +
29A VAL* 4.0 12.8 - - + -
40A VAL* 3.4 32.5 - - + -
41A PRO* 3.7 17.3 - - + -
62A LYS 3.4 4.7 - - - +
63A GLY 3.7 19.1 - - - +
64A THR 3.9 17.0 - - - +
65A TYR* 4.7 3.1 - - + +
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Residues in contact with ASN 28 (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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8A HIS* 3.8 17.6 + - - +
10A GLU* 3.3 14.4 + - - +
15A ALA* 3.3 7.7 - - - +
16A ALA 3.4 9.1 + - - -
17A ASP* 2.8 27.4 + - - +
27A LEU* 1.3 74.6 - - - +
29A VAL* 1.3 60.4 + - - +
62A LYS* 2.8 39.4 + - + +
121A GLN* 2.8 42.8 + - - +
122A GLY 4.4 1.2 + - - -
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Residues in contact with VAL 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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15A ALA* 3.1 6.5 - - - -
16A ALA* 2.8 40.7 + - + +
18A ILE* 4.1 36.6 - - + -
27A LEU* 4.2 7.4 - - + -
28A ASN* 1.3 77.5 - - - +
30A ILE* 1.3 62.8 + - - +
31A VAL* 3.5 0.6 + - + -
38A LEU* 4.8 2.0 - - + -
40A VAL* 4.2 13.9 - - + -
121A GLN* 3.7 0.7 - - - +
122A GLY* 3.3 26.2 - - - +
123A ILE 4.4 0.7 - - - +
124A LEU* 3.7 29.6 - - + +
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Residues in contact with ILE 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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10A GLU* 4.6 0.4 - - - +
13A THR* 3.3 35.9 - - + +
14A TYR 3.7 7.0 - - - +
15A ALA* 4.2 0.4 - - - +
29A VAL* 1.3 71.5 - - - +
31A VAL* 1.3 69.9 + - - +
32A ASP* 3.6 8.0 + - + +
119A ILE* 4.9 3.6 - - + -
120A ASP* 6.2 1.3 - - + -
121A GLN* 3.6 37.7 - - + +
122A GLY 2.9 10.8 + - - +
123A ILE* 3.5 17.3 - - + +
124A LEU* 2.6 33.7 + - - +
220A GLY* 4.9 4.0 - - - -
343A A70 4.0 31.9 - - + -
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Residues in contact with VAL 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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7A LEU* 3.4 33.4 - - + -
14A TYR* 3.2 13.5 + - + +
16A ALA* 3.8 22.2 - - + +
29A VAL 4.3 0.4 - - - +
30A ILE* 1.3 77.2 - - - +
32A ASP* 1.3 55.1 + - - +
33A THR* 5.5 1.3 - - + -
124A LEU* 3.7 17.5 - - + +
126A VAL* 4.3 16.6 - - + -
157A LEU* 5.4 3.8 - - + -
169A ILE* 4.2 27.4 - - + -
171A PHE* 5.9 0.4 - - + -
219A SER* 2.7 32.8 + - - +
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Residues in contact with ASP 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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30A ILE* 3.6 3.8 + - + +
31A VAL* 1.3 73.1 - - - +
33A THR* 1.3 57.8 + - - +
34A GLY 3.2 4.1 + - - -
35A SER* 2.7 36.2 + - - +
84A TYR* 4.0 3.5 - - - -
123A ILE* 3.7 20.6 - - + +
124A LEU 3.0 9.4 + - - +
125A GLY* 3.4 0.5 - - - -
126A VAL* 3.2 23.9 + - - -
218A ASP* 3.0 12.5 - - - +
219A SER* 3.4 0.9 - - - -
220A GLY* 3.3 7.8 - - - +
343A A70 2.5 46.4 + - - +
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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