Contacts of the helix formed by residues 52 - 60 (chain B) in PDB entry 3H1S
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 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B PHE* 5.0 1.3 - - - -
50B GLY 3.9 1.4 + - - -
51B ARG* 1.3 75.6 - - - +
53B LEU* 1.3 64.8 + - - +
54B GLU* 3.4 9.0 + - - +
55B GLU* 2.8 37.0 + - - +
56B ILE* 3.1 17.3 + - - +
302B GOL 3.8 21.9 + - - -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B PHE* 3.8 25.0 - - + -
39B LEU* 3.8 26.5 - - + -
51B ARG 3.7 1.4 + - - -
52B ASN* 1.3 72.8 - - - +
54B GLU* 1.3 58.1 + - + +
56B ILE* 3.2 6.1 + - + +
57B VAL* 2.9 32.2 + - + +
68B ALA* 3.6 25.8 - - + +
71B VAL* 3.7 24.0 - - + -
72B PHE* 3.8 29.4 - - + +
75B THR* 5.9 1.1 - - - +
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ASN* 3.2 8.3 + - - +
53B LEU* 1.3 77.1 - - + +
55B GLU* 1.3 63.3 + - - +
57B VAL* 3.4 4.6 + - - +
58B LYS* 3.0 31.5 + - - +
72B PHE* 4.0 19.8 - - + -
145B LEU* 3.8 34.6 - - + +
302B GOL 3.8 18.9 + - - +
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ARG* 3.1 39.4 + - + +
52B ASN* 2.8 27.1 + - - +
54B GLU* 1.3 75.5 - - - +
56B ILE* 1.3 61.1 + - - +
58B LYS* 3.1 4.2 + - - -
59B THR* 2.7 51.8 + - + +
302B GOL 2.7 43.5 + - - +
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Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B PHE* 3.6 35.0 - - + -
39B LEU* 4.7 2.0 - - + -
43B VAL* 4.5 5.8 - - + -
48B HIS* 3.5 37.2 - - + +
51B ARG* 3.8 14.8 - - + +
52B ASN 3.1 10.9 + - - +
53B LEU* 3.2 7.8 + - + +
55B GLU* 1.3 75.2 - - - +
57B VAL* 1.3 54.2 + - - +
59B THR* 4.0 4.3 - - - -
60B SER* 2.6 41.3 + - - +
64B ILE* 3.5 31.0 - - + -
68B ALA* 3.6 16.4 - - + -
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU 2.9 20.3 + - - +
54B GLU* 3.6 10.1 - - - +
55B GLU 3.3 0.2 - - - -
56B ILE* 1.3 75.9 - - - +
58B LYS* 1.3 60.4 + - - +
59B THR 3.4 0.2 + - - -
60B SER* 4.2 4.1 + - - +
65B PHE* 3.3 33.8 - - + -
68B ALA* 3.7 28.0 - - + +
69B ALA* 3.8 8.7 - - + -
72B PHE* 4.1 15.0 - - + -
143B CYS* 4.0 33.7 - - + -
145B LEU* 4.3 8.7 - - + -
146B THR* 3.4 11.0 - - + +
301B GOL 5.5 0.3 - - - -
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Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B GLU* 3.0 20.0 + - - +
55B GLU* 3.1 5.1 + - - +
57B VAL* 1.3 75.3 - - - +
59B THR* 1.3 67.0 + - + +
60B SER 5.3 0.7 - - - -
145B LEU* 3.8 50.7 - - + +
146B THR* 4.4 14.1 - - - +
148B ASN* 5.2 9.4 + - - +
302B GOL 2.9 43.2 + - - +
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Residues in contact with THR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B HIS* 3.5 23.1 + - - -
51B ARG* 4.8 1.5 + - - -
55B GLU* 2.7 41.7 + - + +
58B LYS* 1.3 90.1 - - + +
60B SER* 1.3 63.2 + - - +
302B GOL 6.0 0.4 - - - +
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Residues in contact with SER 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B HIS* 3.7 15.5 - - - -
56B ILE* 2.6 25.8 + - - +
57B VAL* 4.2 1.6 + - - +
58B LYS 3.8 0.7 - - - +
59B THR* 1.3 81.7 - - - +
61B ASN* 1.3 65.2 + - - +
64B ILE* 3.6 24.2 - - - -
65B PHE* 3.1 27.9 + - - +
301B GOL 3.5 17.8 + - - -
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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