Contacts of the helix formed by residues 60 - 69 (chain A) in PDB entry 4S0H
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 GLU 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A LEU 3.6 0.4 + - - -
59A HIS* 1.3 101.9 + - + +
61A ARG* 1.3 64.7 + - - +
62A GLU* 3.2 6.9 + - - -
63A LEU* 3.3 37.7 + - + +
64A TRP* 3.3 22.6 + - + +
85A PRO* 5.9 2.7 - - + +
86A SER* 5.5 4.0 - - - +
88A LYS* 5.5 5.4 - - - +
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 3.6 31.6 + - + +
59A HIS 3.3 1.4 - - - -
60A GLU* 1.3 76.6 - - - +
62A GLU* 1.3 63.4 + - + +
64A TRP* 3.1 4.2 + - - +
65A LEU* 2.9 53.8 + - + +
208A GLU* 3.9 23.6 + - + +
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Residues in contact with GLU 62 (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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60A GLU* 3.2 3.4 - - - -
61A ARG* 1.3 81.3 - - + +
63A LEU* 1.3 61.8 + - - +
65A LEU* 3.1 12.3 + - - +
66A LYS* 3.0 29.4 + - + +
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Residues in contact with LEU 63 (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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60A GLU* 3.3 42.9 + - + +
61A ARG 3.3 0.4 - - - -
62A GLU* 1.3 76.0 - - - +
64A TRP* 1.3 66.6 + - - +
66A LYS* 3.1 30.4 + - + +
67A PHE* 3.3 27.4 - - + -
84A PHE* 4.3 22.7 - - + -
85A PRO* 4.4 16.2 - - + -
225A LEU* 5.6 0.2 - - + -
229A ASN* 3.2 37.5 - - + +
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Residues in contact with TRP 64 (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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58A LEU* 3.4 34.9 - - + +
59A HIS 3.8 5.4 + - - -
60A GLU* 3.3 20.0 + - + +
61A ARG 3.1 9.7 + - - +
63A LEU* 1.3 77.9 - - - +
65A LEU* 1.3 57.4 + - - +
67A PHE* 2.8 10.9 + - + +
68A HIS* 2.8 27.4 + - - +
72A THR* 4.6 8.3 - - + -
74A MET* 3.8 20.4 - - + -
83A MET* 4.8 8.3 - - - -
85A PRO* 3.7 49.6 - - + +
86A SER 3.5 22.3 + - - -
87A TYR* 4.2 9.4 - + + -
181A PRO* 5.9 0.2 - - + -
208A GLU* 3.8 24.7 - - + +
209A THR* 3.9 36.3 - - + -
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Residues in contact with LEU 65 (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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61A ARG* 2.9 51.1 + - + +
62A GLU* 3.1 12.3 + - - +
64A TRP* 1.3 70.5 - - - +
66A LYS* 1.3 66.6 + - - +
67A PHE 3.0 1.9 + - - -
68A HIS* 4.1 13.5 - - + +
69A GLU* 3.2 41.8 + - + +
208A GLU* 3.6 30.1 - - + -
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Residues in contact with LYS 66 (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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62A GLU* 3.0 21.9 + - - +
63A LEU* 3.1 32.5 + - + +
65A LEU* 1.3 76.3 - - - +
67A PHE* 1.3 59.2 + - + +
69A GLU* 4.1 4.4 + - - +
70A VAL* 3.7 12.1 - - - +
225A LEU* 3.3 33.2 - - + +
229A ASN* 5.1 4.3 - - - +
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Residues in contact with PHE 67 (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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63A LEU* 3.3 36.0 + - + -
64A TRP* 2.8 10.8 + - + +
66A LYS* 1.3 77.3 - - - +
68A HIS* 1.3 58.1 + - - +
69A GLU 3.0 10.3 + - - -
70A VAL* 3.1 13.3 + - - +
71A GLY 3.3 9.0 + - - -
72A THR* 3.4 32.7 + - + +
84A PHE* 4.2 11.2 - + - -
85A PRO* 4.1 20.4 - - + -
222A ILE* 3.7 22.3 - - + +
225A LEU* 3.7 41.1 - - + -
226A LYS* 3.6 41.7 - - + -
229A ASN* 5.0 0.2 - - + -
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Residues in contact with HIS 68 (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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64A TRP 2.8 10.5 + - - +
65A LEU* 3.4 14.8 + - + +
67A PHE* 1.3 76.2 - - - +
69A GLU* 1.3 60.8 + - + +
70A VAL 3.4 1.9 + - - -
71A GLY* 4.2 5.9 + - - -
72A THR* 3.7 9.0 + - - +
207A PRO* 4.0 17.5 + - - +
208A GLU* 3.6 42.7 + - + +
210A ALA* 4.6 13.2 + - + -
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Residues in contact with GLU 69 (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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65A LEU* 3.2 31.7 + - + +
66A LYS* 4.7 3.3 - - - +
67A PHE* 3.0 1.8 - - - +
68A HIS* 1.3 87.4 - - + +
70A VAL* 1.3 66.3 + - + +
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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