Contacts of the helix formed by residues 35 - 46 (chain A) in PDB entry 4H0N
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 ASN 35 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASP* 2.6 21.2 + - - +
34A ILE* 1.3 72.2 - - + +
36A THR* 1.3 60.4 + - - +
37A VAL* 3.4 6.5 + - - +
38A ALA* 2.9 33.6 + - + +
39A ASN* 2.8 35.6 + - - +
312A ARG* 3.3 32.7 + - - +
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Residues in contact with THR 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 ILE 3.6 3.2 + - - +
35A ASN* 1.3 74.7 + - - +
37A VAL* 1.3 65.2 + - - +
39A ASN* 3.8 6.8 - - - +
40A SER* 3.1 22.7 + - - -
53A ASN* 3.6 22.7 - - - +
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Residues in contact with VAL 37 (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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35A ASN* 3.3 9.9 + - - +
36A THR* 1.3 80.0 - - - +
38A ALA* 1.3 66.6 + - - +
40A SER* 2.5 28.2 + - - +
41A VAL* 3.1 9.2 + - + +
305A ILE* 4.7 9.0 - - + -
309A GLN* 3.8 36.6 - - + +
312A ARG* 4.3 5.8 - - - +
313A LEU* 3.7 22.7 - - + -
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Residues in contact with ALA 38 (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 GLY* 3.5 29.0 - - - +
12A ILE* 4.2 1.2 - - - -
33A ASP* 4.6 2.9 - - - +
35A ASN* 2.9 28.9 + - + +
37A VAL* 1.3 77.0 - - - +
39A ASN* 1.3 56.3 + - - +
41A VAL* 3.1 5.6 + - - +
42A TYR* 2.8 28.4 + - - +
313A LEU* 3.6 24.9 - - + -
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Residues in contact with ASN 39 (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 SER* 4.6 0.3 + - - -
11A GLY 4.9 0.7 - - - +
33A ASP* 3.0 44.9 + - - +
35A ASN 2.8 24.2 + - - +
36A THR* 3.8 6.4 - - + +
38A ALA* 1.3 75.3 - - - +
40A SER* 1.3 52.6 + - - +
42A TYR* 3.2 3.2 + - - -
43A LYS* 2.8 32.0 + - - +
51A LEU* 3.3 36.8 - - + +
53A ASN* 3.7 27.9 - - - +
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Residues in contact with SER 40 (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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36A THR 3.1 14.4 + - - -
37A VAL* 2.5 26.3 + - - +
39A ASN* 1.3 76.7 - - - +
41A VAL* 1.3 64.8 + - - +
43A LYS* 3.4 11.1 + - - +
44A HIS* 3.1 22.9 + - - +
302A PRO* 4.5 3.5 - - - +
304A ASN* 5.1 7.1 + - - -
305A ILE* 4.6 8.1 - - - +
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 3.7 15.5 - - + -
37A VAL 3.1 12.9 + - - +
38A ALA 3.4 6.5 - - - +
40A SER* 1.3 82.8 + - - +
42A TYR* 1.3 64.8 + - - +
44A HIS* 3.2 9.7 + - - +
45A ASN* 3.2 19.8 + - - +
299A TYR* 3.6 20.9 - - - +
301A LEU* 3.9 18.6 - - + -
302A PRO* 4.1 13.9 - - + -
305A ILE* 4.1 20.9 - - + -
313A LEU* 3.6 22.2 - - + -
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Residues in contact with TYR 42 (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 GLU* 2.8 30.8 + - - -
10A SER* 4.1 8.5 - - - -
11A GLY 3.7 11.0 - - - +
12A ILE* 4.0 7.4 - - - +
13A GLY* 3.4 34.5 - - - -
16A HIS* 2.8 22.1 + - - -
28A ILE* 4.0 0.7 - - - +
31A ALA* 3.6 9.0 - - + +
38A ALA 2.8 13.0 + - - +
39A ASN* 3.2 11.6 + - - +
41A VAL* 1.3 77.6 - - - +
43A LYS* 1.3 58.3 + - - +
45A ASN 3.3 1.6 + - - -
46A PHE* 2.9 50.4 + + + -
49A THR* 3.4 24.6 - - + +
51A LEU* 4.0 21.1 - - + -
299A TYR* 5.2 0.2 - - - -
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Residues in contact with LYS 43 (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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39A ASN 2.8 16.8 + - - +
40A SER* 3.8 9.6 + - - +
42A TYR* 1.3 75.7 - - - +
44A HIS* 1.3 63.3 + - - +
46A PHE 4.2 9.0 - - - +
47A PRO* 3.2 33.0 - - + +
49A THR 5.6 2.5 - - - +
51A LEU* 4.0 22.2 - - + -
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Residues in contact with HIS 44 (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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40A SER 3.1 13.6 + - - +
41A VAL 3.4 10.3 - - - +
42A TYR 3.1 0.4 - - - -
43A LYS* 1.3 81.4 - - - +
45A ASN* 1.3 63.3 + - - +
47A PRO* 4.0 10.4 - - - +
300A ASN* 3.4 33.2 + - + +
301A LEU 4.5 2.4 + - - -
302A PRO* 3.7 32.3 - - + +
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Residues in contact with ASN 45 (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 LYS* 5.4 1.6 + - - -
41A VAL* 3.2 21.6 + - - +
42A TYR 3.3 2.7 + - - +
44A HIS* 1.3 82.9 - - - +
46A PHE* 1.3 79.9 + - + +
47A PRO* 3.5 7.3 - - - +
48A GLU* 4.5 0.9 - - - +
298A SER 4.0 3.8 - - - +
299A TYR* 3.4 45.9 + - + -
300A ASN* 2.9 43.3 + - - +
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Residues in contact with PHE 46 (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 4.1 10.1 - - - -
13A GLY 3.9 11.9 - - - -
16A HIS* 3.3 44.6 - + + -
17A CYS* 3.9 24.9 - - - -
20A LYS* 4.2 17.5 - - + -
42A TYR* 2.9 48.8 + + + +
43A LYS* 3.5 8.5 - - - +
45A ASN* 1.3 100.0 - - + +
47A PRO* 1.3 63.2 - - - +
48A GLU* 3.0 15.8 + - - +
49A THR* 3.1 28.8 + - - +
299A TYR* 4.2 5.8 - + - -
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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