Contacts of the strand formed by residues 93 - 98 (chain G) in PDB entry 2EWC
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 ALA 93 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64G VAL 2.9 14.4 + - - +
65G GLN* 3.2 6.0 - - + -
66G MSE 2.9 23.2 + - - -
92G PRO* 1.3 76.8 - - - +
94G ARG* 1.3 60.6 + - - +
16L THR 3.4 14.1 - - - +
19L VAL* 3.6 6.0 - - + +
26L TYR* 3.5 22.4 - - + +
27L LEU 3.7 4.5 - - - +
28L ASN* 3.4 25.8 - - - +
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Residues in contact with ARG 94 (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 GLN* 4.2 4.0 - - - +
66G MSE 3.2 23.3 - - + +
68G CYS* 4.2 8.7 - - - -
76G ILE* 4.3 6.3 - - - +
79G MSE 3.6 26.9 - - - +
80G GLU* 2.5 37.7 + - - +
83G ILE* 3.7 15.2 - - - +
92G PRO* 4.6 3.1 - - - +
93G ALA* 1.3 78.7 - - - +
95G LYS* 1.3 63.6 + - - +
96G SER* 4.3 6.3 + - - -
13L ARG 3.1 11.1 + - - -
14L GLY 2.9 30.1 + - - -
15L HIS* 3.5 18.4 - - + +
27L LEU 5.6 0.2 - - - -
28L ASN* 2.8 22.3 + - - +
29L TYR* 3.1 38.8 + - + -
115L ASP* 4.9 1.3 - - - -
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Residues in contact with LYS 95 (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 GLN* 4.3 0.8 - - - +
66G MSE 3.3 3.5 + - - +
67G ASP* 2.7 37.2 + - - +
68G CYS* 2.9 26.7 + - - +
94G ARG* 1.3 78.0 - - - +
96G SER* 1.3 64.1 + - - +
97G ILE* 3.5 30.3 - - + -
95K LYS* 5.8 0.9 - - - +
29L TYR* 4.2 20.0 - - + -
67L ASP* 2.7 37.3 + - - -
69L LEU* 4.0 23.3 - - + -
95L LYS* 5.8 1.6 - - - +
97L ILE* 6.5 0.2 - - - -
113L GLN* 5.5 0.2 - - - +
115L ASP* 2.9 30.0 + - - +
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Residues in contact with SER 96 (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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68G CYS* 3.3 11.2 - - - +
70G PHE* 3.6 21.9 - - - -
73G VAL* 4.2 5.6 - - - +
76G ILE* 3.5 33.1 - - - +
79G MSE 3.9 8.3 - - - +
94G ARG* 4.3 5.5 + - - -
95G LYS* 1.3 77.5 + - - +
97G ILE* 1.3 66.4 + - - +
29L TYR* 5.3 2.6 - - - -
69L LEU* 3.8 13.4 - - - +
99L THR* 4.8 2.3 + - - +
100L GLU 5.3 1.2 - - - +
101L PHE* 5.5 2.6 - - - -
113L GLN* 4.8 3.6 + - - +
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Residues in contact with ILE 97 (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 ASP* 5.4 1.6 - - + -
68G CYS 2.8 9.5 + - - +
69G LEU* 3.5 10.3 - - + -
70G PHE* 2.9 27.7 + - - +
73G VAL* 4.4 4.7 - - - -
95G LYS* 3.5 32.1 - - + +
96G SER* 1.3 79.4 - - - +
98G GLN* 1.3 71.8 + - - +
99G THR* 4.5 10.8 - - + -
95K LYS* 5.3 2.0 - - - -
97K ILE* 4.2 26.2 - - + -
69L LEU* 4.0 14.1 - - + -
95L LYS* 6.3 1.1 - - - -
97L ILE* 3.4 38.8 - - + -
99L THR* 3.8 5.4 - - + +
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Residues in contact with GLN 98 (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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71B ARG* 5.8 0.5 + - - -
100B GLU* 3.0 29.7 + - - +
70G PHE 3.2 6.3 - - - +
71G ARG 3.3 25.9 + - - +
72G ASP* 3.5 6.3 - - - +
73G VAL* 2.8 43.0 + - + +
74G TRP* 4.8 1.9 - - - -
97G ILE* 1.3 79.4 - - - +
99G THR* 1.3 64.8 + - - +
98K GLN 4.7 4.3 - - - +
97L ILE* 5.1 0.2 - - - +
98L GLN 4.7 1.9 - - - +
99L THR* 2.9 24.0 + - - +
100L GLU* 3.7 21.2 + - + +
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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