Contacts of the strand formed by residues 62 - 71 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60G ILE* 4.3 7.0 - - + +
61G GLN* 1.3 76.3 - - - +
63G LEU* 1.3 62.0 + - - +
64G ARG* 3.6 25.6 - - - +
80G TYR* 6.0 0.6 - - - +
82G ASN* 5.1 3.6 + - - +
84G TYR* 3.2 49.6 + - - +
85G GLN* 3.0 36.9 + - - +
86G THR* 2.8 39.8 + - + +
87G MET* 3.3 10.4 + - - +
174G ILE* 6.2 0.9 - - + -
175G VAL 3.3 8.7 - - - +
176G VAL* 4.2 15.9 - - + -
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Residues in contact with LEU 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G ARG* 1.3 79.8 - - - +
64G ARG* 1.3 74.9 + - - +
65G GLY* 4.1 3.1 - - - +
77G ILE* 4.5 7.0 - - + -
79G SER* 3.5 14.8 - - - +
85G GLN* 3.3 8.7 - - - +
87G MET* 3.4 42.0 - - + +
88G GLU 4.3 2.2 - - - +
89G VAL* 3.4 28.0 - - + +
94G VAL* 3.7 25.8 - - + -
173G LEU* 4.7 5.2 - - + +
174G ILE* 3.3 6.8 - - - +
175G VAL* 2.9 34.9 + - + +
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Residues in contact with ARG 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G ARG* 3.6 24.0 - - - +
63G LEU* 1.3 77.4 - - - +
65G GLY* 1.3 59.8 + - - +
79G SER* 3.9 2.3 + - - -
80G TYR* 3.4 52.1 + - + +
85G GLN* 2.8 27.8 + - - -
172G GLU* 3.0 31.2 + - - +
173G LEU 3.4 4.0 - - - -
174G ILE* 4.0 22.0 - - + +
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Residues in contact with GLY 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G LEU* 4.1 1.5 - - - +
64G ARG* 1.3 75.9 - - - +
66G ALA* 1.3 62.3 + - - -
67G VAL* 4.8 0.2 - - - -
77G ILE* 4.1 15.7 - - - -
78G SER 3.3 13.9 - - - -
79G SER* 4.2 0.7 - - - -
80G TYR* 4.0 5.4 - - - -
172G GLU* 3.3 7.2 - - - +
173G LEU 2.8 40.5 + - - +
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Residues in contact with ALA 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G GLY* 1.3 74.1 - - - -
67G VAL* 1.3 61.6 + - - +
68G THR* 4.1 13.6 + - + -
76G PHE 3.4 2.8 - - - +
78G SER* 2.8 47.5 + - - +
80G TYR* 3.6 28.2 - - + +
171G GLY 3.7 7.6 - - - +
172G GLU* 5.2 0.4 - - - -
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Residues in contact with VAL 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G GLY 4.3 1.1 - - - +
66G ALA* 1.3 77.8 - - - +
68G THR* 1.3 63.0 + - - +
69G ARG 4.4 1.3 - - - +
75G LEU* 3.9 26.7 - - + -
76G PHE 3.6 11.4 - - - +
77G ILE* 4.9 7.6 - - + -
106G LEU* 4.6 8.1 - - + -
107G LYS 5.2 1.1 - - - +
110G PHE* 6.3 0.2 - - + -
154G LEU* 5.3 1.3 - - + -
168G ILE* 3.5 34.2 - - + +
171G GLY* 3.0 32.9 + - - +
172G GLU 4.1 4.5 - - - +
173G LEU* 4.0 28.7 - - + +
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Residues in contact with THR 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G ALA* 4.1 11.4 + - + -
67G VAL* 1.3 81.5 - - - +
69G ARG* 1.3 79.1 + - - +
76G PHE* 4.3 3.3 + - - -
78G SER* 6.0 3.1 - - - -
167G GLN* 4.0 3.5 - - - -
168G ILE* 3.0 38.6 + - - +
171G GLY 5.8 0.4 - - - +
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Residues in contact with ARG 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G VAL* 3.9 0.5 - - - +
68G THR* 1.3 90.8 + - - +
70G CYS* 1.3 67.1 + - - +
71G GLU* 3.7 20.2 + - - +
75G LEU* 3.8 3.5 - - - -
76G PHE* 2.9 71.5 + - + +
78G SER* 6.2 0.6 - - - -
166G LEU 4.0 12.6 - - - +
168G ILE* 3.9 11.5 - - - +
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Residues in contact with CYS 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G ARG* 1.3 83.4 - - - +
71G GLU* 1.3 62.4 + - - +
73G GLY* 4.0 3.1 - - - -
74G GLN 3.2 29.4 - - - +
75G LEU* 4.6 3.1 - - + -
156G VAL* 4.1 13.5 - - - -
163G CYS* 2.0 66.1 + - - +
164G GLU* 4.4 5.0 - - - -
166G LEU* 4.0 22.8 + - + -
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Residues in contact with GLU 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G ARG* 3.7 16.7 + - - +
70G CYS* 1.3 75.0 - - - +
72G ASP* 1.3 87.1 + - - +
73G GLY 3.3 1.6 - - - -
74G GLN* 2.7 26.5 + - - +
76G PHE* 3.4 40.4 - - + +
92G ASN* 4.5 3.5 + - - -
163G CYS* 3.9 1.8 - - - -
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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