Contacts of the strand formed by residues 79 - 84 (chain G) in PDB entry 5E94
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 SER 79 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76G GLU* 2.8 44.7 + - - +
77G PRO 4.6 0.9 - - - -
78G GLY* 1.3 80.9 - - - +
80G PHE* 1.3 70.9 + - - +
81G VAL* 3.7 2.9 + - - +
103G PHE* 3.5 6.1 - - - -
104G CYS* 3.0 27.2 + - - +
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Residues in contact with PHE 80 (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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79G SER* 1.3 82.4 + - - +
81G VAL* 1.3 60.6 + - - +
82G ASN* 4.1 16.6 + - - +
101G TYR* 4.8 2.5 - - + -
102G ARG 3.5 15.0 - - - +
103G PHE* 3.7 17.7 - + + -
120G TRP* 4.0 13.9 - + - -
111H LEU* 3.6 35.4 - - + -
112H GLN 4.0 2.7 - - - -
113H LYS* 3.6 56.5 - - + -
114H ASP 5.4 0.4 - - - -
120H TRP* 3.8 25.6 - + - -
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Residues in contact with VAL 81 (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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72G TRP* 3.7 10.8 - - + -
73G PRO* 3.8 36.1 - - + +
74G ASP 5.0 1.1 - - - +
75G GLY* 3.7 26.2 - - - -
76G GLU 4.7 0.4 - - - +
79G SER* 4.1 11.9 - - - +
80G PHE* 1.3 74.7 - - - +
82G ASN* 1.3 68.5 + - - +
100G VAL 3.7 0.7 - - - +
101G TYR* 3.4 8.3 - - - +
102G ARG* 3.0 28.0 + - + +
104G CYS* 4.6 0.7 - - + -
110G TRP* 3.7 24.7 - - + -
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Residues in contact with ASN 82 (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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73G PRO* 5.4 1.7 - - - +
80G PHE* 4.1 13.5 + - - +
81G VAL* 1.3 81.3 - - - +
83G VAL* 1.3 67.7 + - - +
99G HIS* 4.1 18.4 - - + +
100G VAL 3.7 4.0 - - - -
101G TYR* 3.1 31.3 - - + -
113H LYS* 5.5 0.2 - - - -
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Residues in contact with VAL 83 (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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42G TYR* 4.6 5.6 - - - +
70G ALA* 4.2 11.4 - - + -
71G CYS 3.5 28.5 - - - +
72G TRP* 3.7 15.5 - - + -
73G PRO* 3.6 21.8 - - + -
81G VAL* 4.6 0.4 - - + -
82G ASN* 1.3 80.9 - - - +
84G SER* 1.3 73.9 + - - +
99G HIS* 3.2 4.9 - - - -
100G VAL* 2.7 53.2 + - + +
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Residues in contact with SER 84 (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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42G TYR* 5.1 0.9 + - - -
83G VAL* 1.3 88.2 - - - +
85G CYS* 1.3 72.7 + - - +
86G PRO* 3.2 7.4 - - - +
98G GLY 3.5 10.1 - - - -
99G HIS* 3.6 13.5 + - - -
100G VAL* 4.3 0.2 - - - +
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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