Contacts of the strand formed by residues 23 - 29 (chain A) in PDB entry 4HAE
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 TRP 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LYS* 3.7 38.4 - - + -
16A ARG* 3.4 21.5 - - - -
17A LYS* 3.6 45.5 - - + +
21A GLY 4.8 3.8 + - - -
22A LYS* 1.3 79.5 - - - +
24A GLU* 1.3 63.6 + - - +
25A TYR* 4.8 1.8 - - + -
41A PRO* 3.9 1.9 - - - +
42A GLU* 3.1 58.6 + - + +
43A HIS* 6.0 0.2 - - - -
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Residues in contact with GLU 24 (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 LYS* 3.4 7.4 - - - +
16A ARG* 2.8 70.5 + - + +
18A ASN* 3.1 36.6 + - + +
23A TRP* 1.3 79.1 - - - +
25A TYR* 1.3 65.5 + - - +
39A TRP* 3.7 18.0 - - + +
40A GLU 3.1 20.2 - - - +
41A PRO* 4.4 6.9 - - + +
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Residues in contact with TYR 25 (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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12A ILE* 3.5 31.4 - - + -
14A ASP 3.5 7.4 - - - +
15A LYS* 3.4 43.0 + - + -
23A TRP* 4.8 2.2 - - + -
24A GLU* 1.3 77.0 - - - +
26A LEU* 1.3 61.6 + - - +
27A ILE* 3.5 22.2 + - + +
38A THR 3.3 2.4 - - - +
39A TRP* 3.3 5.4 - - - -
40A GLU 2.8 37.4 + - - +
42A GLU* 3.3 46.5 + - + -
45A LEU* 5.2 9.4 - - + -
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Residues in contact with LEU 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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12A ILE* 3.6 3.3 - - - -
13A VAL* 2.7 57.5 + - + +
14A ASP* 3.0 19.8 + - + +
25A TYR* 1.3 71.8 - - - +
27A ILE* 1.3 57.2 + - - +
37A ASP* 3.8 18.8 - - + +
38A THR 3.5 28.5 - - - +
39A TRP* 3.5 48.3 - - + +
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Residues in contact with ILE 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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-1A PHE* 5.2 2.2 - - + -
9A VAL* 3.8 21.3 - - + -
11A ARG 3.9 1.1 - - - -
12A ILE* 3.2 33.7 - - + -
13A VAL* 4.5 0.2 - - - -
25A TYR* 3.7 21.1 - - + +
26A LEU* 1.3 71.6 - - - +
28A ARG* 1.3 71.3 + - - +
29A TRP* 3.5 42.0 + - + -
37A ASP* 3.2 27.4 - - - -
38A THR 2.9 13.1 + - - +
40A GLU* 3.8 21.3 - - + -
45A LEU* 4.9 7.2 - - + -
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Residues in contact with ARG 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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10A GLU* 2.8 48.2 + - + +
11A ARG* 2.9 31.8 + - + +
13A VAL* 3.9 20.0 - - + +
27A ILE* 1.3 76.6 - - - +
29A TRP* 1.3 57.0 + - - +
32A TYR 3.5 24.7 - - - +
33A GLY* 4.0 2.1 - - - -
34A SER* 3.3 18.1 - - - +
37A ASP* 2.7 37.9 + - - -
101A SO4 3.0 43.3 + - - -
102A UNX 3.7 4.0 - - - -
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Residues in contact with TRP 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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-1A PHE* 3.7 43.7 - + + -
7A TYR* 4.0 20.0 - + + -
8A GLU 4.0 11.9 - - - -
9A VAL* 4.2 3.8 - - + -
10A GLU* 4.1 2.0 - - - +
27A ILE* 3.5 31.6 + - + -
28A ARG* 1.3 75.8 - - - +
30A LYS* 1.3 65.5 + - - +
31A GLY 3.3 0.3 + - - -
32A TYR* 3.0 42.5 + + + +
36A GLU* 3.2 25.1 + - + -
38A THR* 3.0 30.0 + - - +
40A GLU* 3.7 15.9 - - + -
102A UNX 3.1 11.8 - - - -
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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