Contacts of the strand formed by residues 63 - 70 (chain H) 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 VAL 63 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27H LEU* 4.9 2.5 - - + -
49H MSE 4.1 15.5 - - + -
53H LEU* 3.6 31.0 - - + -
60H LEU* 3.2 21.4 + - + +
61H ASP 3.3 0.2 - - - -
62H ALA* 1.3 77.3 - - - +
64H VAL* 1.3 62.7 + - - +
65H GLN 3.7 8.5 - - - +
66H MSE 3.7 33.2 - - + -
87H PHE* 4.4 4.0 - - + -
90H ARG 5.7 0.2 - - - +
92H PRO* 3.8 12.1 - - + +
117H VAL 3.6 7.4 - - - +
118H ALA* 4.1 6.1 - - + +
6J ARG* 3.2 24.4 + - - -
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Residues in contact with VAL 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H PHE* 5.1 0.4 - - + -
62H ALA 3.7 13.2 - - - +
63H VAL* 1.3 72.6 - - - +
65H GLN* 1.3 62.3 + - - +
92H PRO* 3.6 5.6 - - - -
93H ALA* 3.0 21.3 + - - +
117H VAL* 2.8 33.3 + - + +
118H ALA* 4.5 2.9 - - - +
119H TYR* 3.8 18.2 - - + -
4J ILE* 3.9 11.2 - - + -
6J ARG* 4.4 0.2 - - - +
19J VAL* 3.5 37.1 - - + +
21J ALA* 3.9 8.3 - - + -
26J TYR* 3.8 30.8 - - + +
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Residues in contact with GLN 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63H VAL* 3.7 1.0 - - - +
64H VAL* 1.3 82.3 - - + +
66H MSE 1.3 88.7 + - - +
67H ASP* 2.8 34.0 + - - +
92H PRO* 3.7 1.2 - - - +
93H ALA* 3.2 15.1 + - + +
94H ARG* 4.3 4.4 - - - +
95H LYS* 4.1 1.5 - - - +
115H ASP* 5.0 0.2 - - - +
116H GLY* 3.1 5.5 - - - -
117H VAL* 2.9 44.0 + - + +
26J TYR* 3.8 33.4 - - + -
27J LEU 5.3 4.0 + - - +
115J ASP* 4.1 13.1 + - - +
116J GLY 6.0 0.7 - - - +
117J VAL* 6.2 0.2 - - + -
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Residues in contact with MSE 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H PHE* 3.6 33.4 - - + -
49H MSE 4.0 10.1 - - + +
63H VAL* 3.7 13.5 - - + -
65H GLN* 1.3 94.9 + - - +
67H ASP* 1.3 58.3 + - - +
68H CYS* 4.1 12.8 - - - -
83H ILE* 4.0 23.1 - - + -
87H PHE* 3.7 18.2 - - + -
92H PRO* 3.7 18.6 - - + -
93H ALA 3.0 7.9 + - - +
94H ARG* 3.2 23.7 - - + +
95H LYS 3.3 3.8 + - - +
114H VAL* 4.0 8.5 - - + -
115H ASP 3.2 12.8 - - - +
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Residues in contact with ASP 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H GLN* 2.8 21.1 + - - +
66H MSE 1.3 71.5 - - - +
68H CYS* 1.3 61.3 + - - +
69H LEU* 4.1 5.9 + - + +
95H LYS* 2.8 45.5 + - + +
97H ILE* 5.1 2.5 - - + -
114H VAL* 3.3 4.3 - - - +
115H ASP* 2.9 43.5 + - - +
67I ASP* 4.8 0.7 - - - +
95I LYS* 2.7 36.8 + - + +
67J ASP* 4.7 2.1 - - - +
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Residues in contact with CYS 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H MSE 4.2 15.3 - - - -
67H ASP* 1.3 75.4 - - - +
69H LEU* 1.3 62.6 + - - +
70H PHE* 3.7 8.4 - - + -
79H MSE 3.3 39.7 - - - -
94H ARG* 4.2 7.2 - - - -
95H LYS 3.0 11.0 + - - -
96H SER* 3.3 13.3 - - - +
97H ILE* 2.8 29.1 + - - +
112H PHE* 4.1 3.8 - - + -
113H GLN 3.7 4.7 - - - -
114H VAL* 4.1 13.7 - - - -
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Residues in contact with LEU 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H TYR* 5.4 0.9 - - + -
67H ASP 4.8 2.2 - - - +
68H CYS* 1.3 83.6 - - - +
70H PHE* 1.3 61.4 + - - +
97H ILE* 3.5 25.4 - - + -
99H THR* 3.6 14.6 - - + -
101H PHE* 3.7 14.2 - - + -
112H PHE* 3.4 8.1 - - - -
113H GLN* 2.8 61.4 + - + +
114H VAL* 6.2 0.9 - - - -
95I LYS* 3.9 33.7 - - + -
96I SER 3.8 19.5 - - - +
97I ILE* 4.2 8.5 - - + -
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Residues in contact with PHE 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ILE* 4.7 4.9 - - + -
42H ILE* 4.5 4.0 - - + -
68H CYS* 3.7 18.6 - - + -
69H LEU* 1.3 77.4 - - - +
71H ARG* 1.3 59.3 + - - +
72H ASP 3.6 29.6 - - - +
73H VAL* 3.7 11.0 - - + +
75H ASN* 3.7 27.8 - - + -
76H ILE* 3.7 15.0 - - + -
79H MSE 3.8 22.2 - - + -
96H SER* 3.6 26.9 - - - -
97H ILE 2.8 14.1 + - - +
98H GLN* 3.2 5.2 - - - -
99H THR 2.8 27.1 + - - -
101H PHE* 4.1 2.0 - - - -
111H LEU 3.7 2.9 - - - -
112H PHE* 3.6 28.9 - + - -
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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