Contacts of the strand formed by residues 27 - 33 (chain G) in PDB entry 2WA9
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 MET 27 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25G PRO 4.1 4.2 + - - +
26G SER* 1.3 74.5 - - - +
28G TYR* 1.3 70.7 + - - +
75G VAL* 3.7 26.2 - - + +
76G PHE* 3.3 38.6 - - - +
77G THR* 3.8 18.2 - - + +
105G LYS* 4.9 1.7 - - - +
106G ALA* 4.2 23.7 + - + +
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Residues in contact with TYR 28 (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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26G SER* 3.7 29.6 - - - -
27G MET* 1.3 87.6 - - - +
29G LYS* 1.4 63.5 + - - +
30G VAL* 3.4 6.1 + - - +
75G VAL* 4.1 4.0 - - - -
76G PHE* 2.6 33.6 + - - +
78G ALA* 3.8 20.2 - - + -
81G ALA* 3.8 21.3 - - + -
103G LEU* 3.9 23.6 - - + -
104G GLU 2.6 33.2 - - - +
105G LYS* 2.6 35.8 + - + +
106G ALA 5.0 0.2 - - - +
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Residues in contact with LYS 29 (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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28G TYR* 1.4 70.6 - - - +
30G VAL* 1.3 61.5 + - - +
31G ILE* 3.8 20.9 + - + +
72G ILE* 4.2 26.8 - - + +
74G GLY 3.9 4.7 - - - -
75G VAL* 4.3 11.3 - - + +
102G THR 3.7 3.5 - - - +
103G LEU* 3.8 4.0 - - - +
104G GLU* 3.3 41.4 + - + +
105G LYS 4.6 0.7 - - - -
106G ALA* 3.1 49.3 - - + +
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Residues in contact with VAL 30 (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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28G TYR 4.1 0.4 - - - +
29G LYS* 1.3 71.5 - - - +
31G ILE* 1.3 56.1 + - - +
51G PHE* 3.8 28.0 - - + -
72G ILE 3.5 2.1 - - - -
73G CYS* 2.7 33.4 + - + +
74G GLY 2.8 17.5 + - - +
76G PHE* 3.6 26.9 - - + -
81G ALA* 3.8 33.0 - - + +
84G LYS* 4.6 8.7 - - + -
85G VAL* 4.6 5.4 - - + -
101G CYS* 3.9 18.2 - - - -
102G THR 3.7 4.0 - - - +
103G LEU* 4.7 0.4 - - + -
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Residues in contact with ILE 31 (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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29G LYS* 4.0 20.0 - - + +
30G VAL* 1.3 76.8 - - - +
32G LEU* 1.3 75.2 + - - +
33G VAL* 4.3 3.1 - - + -
70G LYS* 4.0 28.3 - - + +
71G ALA 3.6 9.2 - - - +
72G ILE* 3.9 21.1 - - + -
101G CYS* 3.4 5.1 - - - -
102G THR* 2.7 56.5 + - + +
104G GLU* 3.8 38.8 - - + +
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Residues in contact with LEU 32 (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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31G ILE* 1.3 74.0 - - - +
33G VAL* 1.3 60.9 + - - +
43G VAL* 4.0 28.0 - - + -
46G VAL* 4.4 15.5 - - + -
47G LEU* 4.5 5.4 - - + -
51G PHE* 5.1 1.1 - - + -
65G VAL* 3.7 17.3 - - + +
70G LYS* 3.2 6.1 - - - +
71G ALA 2.9 35.5 + - - +
73G CYS* 3.7 23.8 - - - -
88G VAL* 4.2 11.2 - - + -
99G LEU* 4.4 18.2 - - + -
100G LEU 4.1 0.4 - - - -
101G CYS* 3.4 34.3 - - + -
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Residues in contact with VAL 33 (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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31G ILE* 4.3 6.1 - - + +
32G LEU* 1.3 76.6 - - - +
34G ASN* 1.3 71.4 + - - +
35G ASP* 3.9 2.8 - - - +
65G VAL* 4.0 3.1 - - - -
69G GLY 3.7 11.4 - - - +
70G LYS* 4.3 7.6 - - + -
99G LEU* 3.6 18.9 - - - +
100G LEU* 2.9 36.3 + - + +
102G THR* 4.0 27.6 - - + -
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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