Contacts of the helix formed by residues 22 - 32 (chain A) in PDB entry 5U07
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 THR 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PHE 4.4 5.5 - - - +
21A ARG* 1.3 87.0 - - + +
23A ALA* 1.3 69.3 + - - +
24A GLY 3.8 3.1 + - - +
25A ASN* 3.5 29.7 + - + +
26A LEU* 3.1 22.2 + - - +
171A VAL* 3.7 7.4 - - - +
172A ARG 2.7 41.6 + - - +
174A PRO* 4.0 15.0 - - + -
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Residues in contact with ALA 23 (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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22A THR* 1.3 76.0 + - - +
24A GLY* 1.3 65.5 + - - +
26A LEU* 2.8 40.4 + - + +
27A HIS* 2.9 6.2 + - - +
169A ASP* 5.0 4.9 - - - +
171A VAL* 3.3 27.7 - - + +
215A SER 5.0 0.9 - - - +
216A TYR* 3.7 30.7 - - + +
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Residues in contact with GLY 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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22A THR* 3.4 6.4 + - - -
23A ALA* 1.3 77.4 - - - +
25A ASN* 1.3 61.1 + - - +
27A HIS* 3.1 10.3 + - - +
28A ARG* 3.0 22.2 + - - +
171A VAL* 5.2 0.8 - - - +
172A ARG 5.8 0.2 - - - -
173A ASP* 3.9 21.2 + - - -
174A PRO* 5.3 0.9 - - - -
180A SER* 5.5 0.9 - - - -
216A TYR* 4.9 7.8 - - - -
61K G 5.2 7.2 - - - -
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Residues in contact with ASN 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 ARG* 5.7 1.0 - - - +
17A ARG 5.3 1.2 + - - -
20A PHE* 4.8 13.4 - - - +
21A ARG* 4.1 28.4 - - - +
22A THR* 3.5 28.3 - - + +
23A ALA 3.2 0.4 - - - -
24A GLY* 1.3 75.9 - - - +
26A LEU* 1.3 56.8 + - - +
28A ARG* 2.9 38.5 + - - +
29A LYS* 2.8 39.3 + - - +
174A PRO* 4.7 10.8 - - + +
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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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20A PHE* 4.6 30.5 - - + +
22A THR 3.1 11.3 + - - +
23A ALA* 2.8 36.7 + - + +
25A ASN* 1.3 74.1 - - - +
27A HIS* 1.3 68.4 + - - +
29A LYS* 3.3 6.1 + - - +
30A LEU* 2.9 48.8 + - + +
53A PHE* 5.5 2.0 - - + -
55A ILE* 5.1 14.4 - - + -
215A SER 4.2 14.8 - - - +
216A TYR 4.8 4.7 - - - +
217A GLY* 4.7 13.2 - - - +
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Residues in contact with HIS 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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23A ALA 2.9 9.9 + - - +
24A GLY* 3.3 11.7 - - - +
26A LEU* 1.3 80.4 - - - +
28A ARG* 1.3 66.7 + - - +
30A LEU* 3.1 8.1 + - - +
31A ILE* 2.9 55.8 + - + +
53A PHE* 5.9 4.3 - + - -
179A ARG* 5.4 4.4 + - - -
215A SER* 3.4 39.0 - - - +
216A TYR* 6.4 1.1 - - + -
61K G 3.0 44.0 + - - +
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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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12A ARG* 4.4 6.7 - - - +
24A GLY 3.0 15.7 + - - +
25A ASN* 2.9 40.5 + - - +
27A HIS* 1.3 76.9 + - - +
29A LYS* 1.3 89.0 + - - +
31A ILE* 3.1 15.7 - - + +
32A ARG* 2.9 33.0 + - + +
174A PRO* 5.4 7.4 - - - +
176A THR* 5.4 9.8 + - - -
179A ARG* 3.3 33.0 - - + +
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Residues in contact with LYS 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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9A PRO* 5.6 10.8 - - + -
12A ARG* 3.0 37.4 - - - +
20A PHE* 5.5 7.9 - - + +
25A ASN* 2.8 34.3 + - - +
26A LEU* 3.7 6.3 - - - +
28A ARG* 1.3 114.0 - - - +
30A LEU* 1.3 64.3 + - + +
32A ARG* 3.0 64.1 + - - +
33A LEU* 3.8 11.6 - - - +
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Residues in contact with LEU 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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7A ILE* 4.1 26.2 - - + -
9A PRO* 5.9 8.3 - - + -
26A LEU* 2.9 39.9 + - + +
27A HIS* 3.5 5.6 - - - +
29A LYS* 1.3 80.0 - - + +
31A ILE* 1.3 63.6 + - + +
33A LEU* 3.1 30.9 - - + +
34A SER* 4.3 2.1 + - - -
51A LEU* 5.4 1.6 - - - +
53A PHE* 3.3 57.7 - - + -
66A VAL* 5.1 3.8 - - + -
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Residues in contact with ILE 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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27A HIS* 2.9 47.6 + - + +
28A ARG* 3.1 19.5 - - + +
30A LEU* 1.3 78.9 - - + +
32A ARG* 1.3 61.8 + - + +
33A LEU 3.1 0.9 - - - -
34A SER* 3.0 30.6 + - - +
37A LEU* 3.8 17.1 - - + +
53A PHE* 5.8 4.5 - - + -
179A ARG* 3.7 27.1 - - - +
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Residues in contact with ARG 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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9A PRO* 6.1 3.6 - - - +
12A ARG* 4.3 9.7 - - - +
28A ARG* 2.9 15.8 + - + +
29A LYS* 3.0 74.0 + - - +
31A ILE* 1.3 77.9 - - + +
33A LEU* 1.3 59.9 + - - +
34A SER 3.3 5.9 + - - +
75A ASP* 3.1 41.1 + - - +
76A ARG* 3.7 25.3 + - - +
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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