Contacts of the helix formed by residues 65 - 78 (chain A) in PDB entry 1FRH
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 GLN 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A GLU 4.8 2.6 + - - -
60A VAL* 3.0 40.0 + - - +
61A PRO 3.5 4.1 + - - +
62A GLU* 3.2 25.6 + - + +
64A MET* 1.3 76.9 - - - +
66A GLU* 1.3 64.0 + - - +
67A PHE 3.2 0.5 + - - -
68A ILE* 3.3 36.4 + - - +
69A GLN* 4.3 1.7 + - - +
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Residues in contact with GLU 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 4.5 0.9 - - - +
63A ASP 3.0 28.3 - - - +
64A MET 3.0 9.0 + - - -
65A GLN* 1.3 80.7 + - - +
67A PHE* 1.3 80.7 + - + +
68A ILE 3.1 0.9 + - - -
69A GLN* 3.4 7.9 + - - +
70A LEU* 3.1 25.0 + - + +
101A LEU* 4.0 20.2 - - + +
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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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3A VAL* 3.8 3.4 - - + -
4A VAL 3.7 22.4 - - - +
5A THR* 3.8 13.9 - - + -
6A ASP* 3.7 44.4 - - + -
9A ILE* 4.0 6.1 - - + -
31A PHE* 4.0 16.4 - + - -
60A VAL* 5.1 0.2 - - + -
64A MET* 2.9 30.3 + - + +
66A GLU* 1.3 99.4 - - + +
68A ILE* 1.3 56.7 + - - +
70A LEU* 3.9 13.7 - - + -
71A ASN* 2.8 37.7 + - - -
101A LEU* 3.7 31.0 - - + -
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Residues in contact with ILE 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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3A VAL* 3.9 13.8 - - + +
36A PRO* 5.8 1.0 - - - +
57A GLU* 3.9 48.7 - - + +
60A VAL* 4.0 21.1 - - + -
65A GLN* 3.6 37.7 - - - +
66A GLU 3.1 0.8 + - - -
67A PHE* 1.3 78.2 - - - +
69A GLN* 1.3 61.4 + - - +
71A ASN* 3.5 4.3 + - - +
72A ALA* 3.4 16.5 + - - +
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Residues in contact with GLN 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 GLN 4.3 1.9 + - - +
66A GLU* 3.4 7.7 + - - +
68A ILE* 1.3 76.6 - - - +
70A LEU* 1.3 64.5 + - - +
72A ALA* 3.2 9.3 + - + +
73A GLU* 3.0 47.6 + - + +
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Residues in contact with LEU 70 (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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31A PHE* 4.4 7.9 - - + -
33A VAL* 4.7 0.4 - - - -
66A GLU* 3.1 17.7 + - + +
67A PHE* 3.2 26.9 + - + +
69A GLN* 1.3 76.9 - - - +
71A ASN* 1.3 62.0 + - - +
73A GLU* 3.4 7.0 + - + +
74A LEU* 2.9 63.0 + - + +
101A LEU* 3.9 28.7 - - + -
104A LEU* 4.5 8.5 - - + -
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Residues in contact with ASN 71 (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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2A TYR 5.4 0.7 - - - +
3A VAL* 3.7 11.7 - - + +
4A VAL* 2.8 47.5 + - - +
31A PHE* 4.2 4.6 - - - -
33A VAL* 3.5 24.0 - - + +
34A ILE 3.2 31.1 + - - +
36A PRO* 5.3 2.0 - - + -
67A PHE* 2.8 31.7 + - - +
68A ILE 3.7 5.4 - - - +
70A LEU* 1.3 71.5 - - - +
72A ALA* 1.3 62.2 + - - +
75A ALA* 3.1 28.1 + - - +
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Residues in contact with ALA 72 (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 HIS* 5.8 0.2 - - - -
36A PRO* 3.8 28.3 - - + +
68A ILE 3.4 9.2 + - - +
69A GLN* 3.2 14.9 + - + +
71A ASN* 1.3 81.0 - - - +
73A GLU* 1.3 63.5 + - + +
75A ALA* 3.7 5.5 + - - +
76A GLU* 3.5 20.3 + - - +
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Residues in contact with GLU 73 (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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69A GLN* 3.0 43.7 + - + +
70A LEU* 3.9 7.0 - - + +
72A ALA* 1.3 75.2 - - + +
74A LEU* 1.3 68.0 + - + +
76A GLU* 3.2 22.6 + - - +
77A VAL* 3.8 7.7 + - - +
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Residues in contact with LEU 74 (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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31A PHE* 4.5 1.6 - - + -
33A VAL* 4.1 13.9 - - + -
70A LEU* 2.9 47.6 + - + +
73A GLU* 1.3 80.5 - - + +
75A ALA* 1.3 56.2 + - - +
76A GLU 3.1 0.2 - - - -
77A VAL* 2.9 19.5 + - + +
78A TRP* 2.8 77.1 + - + +
104A LEU* 4.1 14.8 - - + -
106A ARG* 4.5 19.1 - - + +
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Residues in contact with ALA 75 (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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26A TYR* 3.7 32.0 - - + -
33A VAL* 3.9 11.6 - - + +
35A HIS* 3.7 42.9 - - + -
36A PRO* 4.6 0.4 - - + -
71A ASN 3.1 20.3 + - - +
72A ALA 3.9 5.6 - - - +
73A GLU 3.2 0.4 - - - -
74A LEU* 1.3 77.5 - - - +
76A GLU* 1.3 59.6 + - - +
77A VAL 3.5 0.3 + - - -
78A TRP 3.9 2.3 - - - +
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Residues in contact with GLU 76 (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 HIS* 2.9 34.7 + - - -
37A ASP* 4.8 1.9 - - - +
72A ALA 3.5 16.5 - - - +
73A GLU* 3.2 11.2 + - - +
74A LEU 3.1 0.2 - - - -
75A ALA* 1.3 80.2 - - - +
77A VAL* 1.3 65.2 + - + +
78A TRP 5.0 0.4 - - - +
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Residues in contact with VAL 77 (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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73A GLU 4.0 5.4 - - - +
74A LEU* 3.2 37.2 - - + +
76A GLU* 1.3 83.8 - - + +
78A TRP* 1.3 73.8 + - + +
79A PRO* 4.1 2.8 - - - +
106A ARG* 3.5 33.4 - - - +
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Residues in contact with TRP 78 (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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26A TYR* 3.1 30.7 - - + -
27A GLU 3.4 12.1 - - - +
28A GLY* 3.4 24.8 - - - -
29A PRO* 5.4 0.2 - - + -
31A PHE* 3.7 48.5 - + + -
33A VAL* 3.8 26.9 - - + -
74A LEU* 2.8 34.2 + - + +
75A ALA 3.9 2.4 - - - +
76A GLU 5.0 0.2 - - - -
77A VAL* 1.3 93.3 - - + +
79A PRO* 1.3 63.9 - - + +
104A LEU* 4.8 2.5 - - + -
105A GLU 3.5 24.0 - - - -
106A ARG* 3.0 30.8 + - + +
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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