Contacts of the strand formed by residues 62 - 71 (chain F) in PDB entry 2HEY
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 ARG 62 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60F ILE* 4.2 7.4 - - + +
61F GLN* 1.3 76.4 - - - +
63F LEU* 1.3 63.3 + - - +
64F ARG* 3.6 24.9 - - - +
80F TYR* 6.2 0.2 - - - +
82F ASN* 5.3 1.8 + - - +
84F TYR* 3.2 48.0 + - - +
85F GLN* 3.0 30.0 + - - +
86F THR* 2.8 41.0 + - + +
87F MET* 3.3 11.8 + - - +
174F ILE* 6.1 0.9 - - + -
175F VAL 3.3 9.2 - - - +
176F VAL* 4.1 15.9 - - + -
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Residues in contact with LEU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F ARG* 1.3 78.8 - - - +
64F ARG* 1.3 74.1 + - - +
65F GLY* 4.1 3.8 - - - +
77F ILE* 4.5 7.2 - - + -
79F SER* 3.6 13.9 - - - +
85F GLN* 3.2 9.0 - - - +
87F MET* 3.4 42.8 - - + +
88F GLU 4.3 2.2 - - - -
89F VAL* 3.6 27.4 - - + +
94F VAL* 3.7 29.2 - - + -
173F LEU* 4.8 4.7 - - + +
174F ILE* 3.4 7.2 - - - +
175F VAL* 2.9 33.8 + - + +
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Residues in contact with ARG 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F ARG* 3.6 22.6 - - - +
63F LEU* 1.3 78.8 - - - +
65F GLY* 1.3 61.1 + - - +
79F SER* 3.9 2.4 + - - -
80F TYR* 3.3 49.1 + - + +
85F GLN* 2.7 32.7 + - - +
172F GLU* 2.8 36.5 + - - -
173F LEU 3.4 3.6 - - - -
174F ILE* 3.9 21.5 - - + -
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Residues in contact with GLY 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F LEU* 4.1 2.0 - - - +
64F ARG* 1.3 75.1 - - - +
66F ALA* 1.3 61.7 + - - -
67F VAL* 4.9 0.2 - - - -
77F ILE* 4.2 14.4 - - - -
78F SER 3.2 16.4 - - - -
79F SER* 4.1 1.6 - - - -
80F TYR* 3.9 7.9 - - - -
172F GLU* 3.3 5.9 - - - +
173F LEU 2.9 35.0 + - - +
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Residues in contact with ALA 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F GLY* 1.3 74.7 - - - -
67F VAL* 1.3 63.2 + - - +
68F THR* 4.1 10.7 + - - +
76F PHE 3.4 3.6 - - - +
77F ILE* 3.7 0.3 - - - -
78F SER* 2.8 46.4 + - - +
80F TYR* 3.5 28.8 - - + +
171F GLY 3.4 9.2 - - - +
172F GLU* 5.2 0.4 - - - -
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Residues in contact with VAL 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F GLY 4.3 1.3 - - - +
66F ALA* 1.3 79.1 - - - +
68F THR* 1.3 61.8 + - - +
69F ARG 4.4 1.3 - - - +
75F LEU* 3.8 28.3 - - + -
76F PHE 3.7 11.7 - - - +
77F ILE* 5.0 7.6 - - + -
106F LEU* 4.5 9.6 - - + -
110F PHE* 6.2 0.4 - - + -
154F LEU* 5.4 1.3 - - + -
168F ILE* 3.5 34.4 - - + +
171F GLY* 2.9 35.4 + - - +
172F GLU 4.1 11.7 - - - +
173F LEU* 4.1 20.0 - - + +
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Residues in contact with THR 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F ALA* 4.1 9.8 + - - +
67F VAL* 1.3 78.5 + - - +
69F ARG* 1.3 70.3 + - + +
76F PHE* 4.3 2.6 + - - -
78F SER* 5.8 0.2 + - - -
166F LEU 4.3 0.2 - - - +
167F GLN* 4.1 3.3 - - - -
168F ILE* 3.2 38.0 + - - +
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Residues in contact with ARG 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F VAL* 3.8 0.7 - - - +
68F THR* 1.3 87.5 - - + +
70F CYS* 1.3 68.9 + - - +
71F GLU* 2.7 36.8 + - - +
75F LEU* 3.9 2.8 - - - -
76F PHE* 3.0 67.2 + - + +
166F LEU 4.0 12.3 - - - +
168F ILE* 3.9 13.1 - - - +
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Residues in contact with CYS 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ARG* 1.3 83.8 + - - +
71F GLU* 1.3 60.9 + - - +
73F GLY 4.0 0.9 - - - -
74F GLN 3.3 28.5 - - - +
75F LEU* 4.4 2.0 - - + +
156F VAL* 3.9 16.4 - - + -
163F CYS* 2.0 68.8 + - - +
164F GLU* 4.9 4.7 - - - +
166F LEU* 4.2 18.9 + - + -
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Residues in contact with GLU 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ARG* 2.7 32.6 + - - +
70F CYS* 1.3 74.7 - - - +
72F ASP* 1.3 87.4 + - - +
73F GLY 3.3 0.9 - - - -
74F GLN* 2.7 26.3 + - - +
76F PHE* 3.4 31.3 - - + +
92F ASN* 4.7 7.0 + - - +
163F CYS* 4.1 0.7 - - - -
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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