Contacts of the strand formed by residues 61 - 71 (chain G) in PDB entry 3STJ
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 PHE 61 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31G VAL* 3.7 24.7 - - + -
32G GLU* 3.4 6.8 - - - +
33G GLY* 3.2 35.1 + - - +
34G THR 3.3 45.3 - - - -
59G GLN 4.6 1.1 - - - +
60G PRO* 1.4 74.5 - - - +
62G GLU* 1.3 67.5 + - - +
63G GLY* 3.9 11.2 - - - -
83G VAL 5.8 0.4 - - - -
86G GLN* 3.7 44.2 - - + -
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Residues in contact with GLU 62 (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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30G ARG* 3.1 32.6 + - + +
31G VAL 3.3 3.6 - - - +
32G GLU* 3.1 38.0 - - + +
61G PHE* 1.3 77.5 - - - +
63G GLY* 1.3 59.7 + - - +
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Residues in contact with GLY 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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29G VAL 4.6 0.2 - - - -
30G ARG* 3.6 6.1 - - - +
31G VAL* 2.8 43.0 + - - +
61G PHE* 3.9 12.3 - - - -
62G GLU* 1.3 73.6 - - - +
64G LEU* 1.3 61.6 + - - +
83G VAL* 5.8 3.1 - - - -
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Residues in contact with LEU 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G SER* 4.1 11.0 - - - +
29G VAL 3.5 6.7 - - - +
30G ARG* 4.4 22.9 - - + +
62G GLU 4.5 0.2 + - - -
63G GLY* 1.3 72.4 - - - +
65G GLY* 1.3 72.0 + - - +
83G VAL* 5.0 3.1 - - - +
146G ASN* 3.8 29.8 - - + +
149G GLY* 4.2 16.6 - - - +
185G GLY* 4.0 14.1 - - - -
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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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28G SER* 3.6 5.7 - - - -
29G VAL* 2.8 27.2 + - - +
64G LEU* 1.3 82.3 - - - +
66G SER* 1.3 66.0 + - - -
83G VAL* 4.0 16.6 - - - +
146G ASN* 3.8 1.6 - - - +
185G GLY* 3.4 13.2 - - - +
187G SER* 3.9 6.1 - - - -
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Residues in contact with SER 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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26G VAL* 5.1 0.4 - - - -
27G VAL 3.5 12.1 + - - -
29G VAL* 3.3 9.6 - - - +
65G GLY* 1.3 72.9 + - - -
67G GLY* 1.3 55.4 + - - +
79G THR* 2.6 29.0 + - - -
145G GLY* 3.3 5.7 - - - -
146G ASN* 2.9 22.7 + - - +
185G GLY 2.9 19.2 + - - -
186G ASN* 4.0 0.8 - - - -
187G SER 2.8 7.8 + - - -
188G GLY* 3.2 7.9 - - - -
189G GLY* 3.4 26.2 - - - -
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Residues in contact with GLY 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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26G VAL* 3.4 11.3 - - - +
27G VAL* 3.0 42.3 + - - +
29G VAL* 3.8 2.8 - - - +
66G SER* 1.3 76.0 - - - +
68G VAL* 1.3 63.9 + - - -
77G VAL* 3.9 5.8 - - - -
78G LEU 3.3 12.1 - - - -
79G THR* 4.3 0.4 - - - -
188G GLY 3.6 3.1 - - - -
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Residues in contact with VAL 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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25G ALA 3.6 6.1 - - - +
26G VAL* 4.7 0.9 - - + +
67G GLY* 1.3 80.1 - - - +
69G ILE* 1.4 63.9 + - - +
70G ILE* 3.3 3.6 + - + +
77G VAL* 3.3 5.8 - - - +
78G LEU* 2.8 40.2 + - + +
127G ILE* 3.7 42.0 - - + -
188G GLY 3.7 2.5 - - - +
190G ALA* 3.7 35.0 - - + +
198G LEU* 4.1 9.0 - - + -
201G ILE* 3.7 25.4 - - + -
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Residues in contact with ILE 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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24G PRO 4.0 8.3 - - - +
25G ALA 2.8 17.1 + - - +
27G VAL* 3.6 25.4 - - + -
68G VAL* 1.4 68.3 - - - +
70G ILE* 1.3 60.3 + - - +
71G ASN 3.8 6.3 - - - +
72G ALA* 3.8 28.5 - - - +
76G TYR 3.5 7.2 - - - +
77G VAL* 3.9 18.8 - - + -
94G LEU* 4.2 7.0 - - + -
118G ILE* 4.5 2.9 - - + -
124G LEU* 3.9 25.8 - - + -
125G THR 3.3 28.0 - - - +
126G GLN* 3.4 1.2 - - - -
127G ILE* 2.9 32.4 + - - +
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Residues in contact with ILE 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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68G VAL* 3.3 7.1 + - + +
69G ILE* 1.3 73.6 - - - +
71G ASN* 1.4 61.7 + - + +
76G TYR* 2.8 31.9 + - + +
78G LEU* 3.6 32.3 - - + -
115G LEU* 4.3 11.2 - - + -
126G GLN* 3.9 17.5 - - - +
127G ILE* 4.4 11.8 - - + +
129G ILE* 3.7 35.1 - - + +
198G LEU* 5.3 2.2 - - + -
225G ARG* 4.8 6.5 - - + -
228G ALA* 4.1 15.0 - - + -
232G ILE* 6.1 1.6 - - + -
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Residues in contact with ASN 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 ILE* 3.8 4.1 - - - +
70G ILE* 1.4 81.6 - - + +
72G ALA* 1.4 52.5 + - - +
73G SER* 3.1 14.6 + - - -
74G LYS* 2.9 45.8 + - - +
75G GLY* 2.8 31.4 + - - -
76G TYR* 3.0 34.7 + - + -
126G GLN* 3.4 7.9 + - - +
232G ILE* 6.0 2.0 - - - +
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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