Contacts of the strand formed by residues 33 - 38 (chain G) in PDB entry 2JIX
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 LEU 33 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4G LEU* 4.6 0.9 - - + -
23G CYS* 4.1 19.3 - - - -
29G ILE* 4.0 12.6 - - + -
31G ASN 3.0 5.4 + - - +
32G ASP* 1.3 78.3 - - - +
34G GLY* 1.3 66.1 + - - +
35G TRP* 3.3 36.8 - - + +
48G ILE 3.9 0.5 - - - +
49G TYR 3.7 1.0 - - - -
50G ALA* 3.3 9.6 + - - +
51G ALA* 2.8 37.6 + - - +
71G PHE* 3.1 48.5 - - + -
88G CYS* 4.5 1.8 - - + -
89G LEU 3.3 13.0 - - - +
91G HIS* 4.1 5.2 - - - -
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Residues in contact with GLY 34 (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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33G LEU* 1.3 79.8 - - - +
35G TRP* 1.3 61.2 + - - -
36G TYR* 3.4 23.1 - - - -
46G ARG* 5.8 0.2 - - - -
48G ILE 3.0 10.8 - - - -
49G TYR* 4.5 2.9 - - - -
88G CYS* 3.2 4.5 - - - -
89G LEU* 2.8 38.3 + - - +
91G HIS* 5.1 0.8 + - - -
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Residues in contact with TRP 35 (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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6G GLN* 4.3 4.9 - - - -
21G ILE* 3.8 33.0 - - + -
22G THR 4.1 0.4 - - - -
23G CYS* 3.6 32.1 - - + -
33G LEU* 3.3 27.5 - - + +
34G GLY* 1.3 71.7 - - - -
36G TYR* 1.3 66.6 + - - +
46G ARG* 3.7 2.8 - - - +
47G LEU* 2.9 25.2 + - + -
48G ILE* 2.9 35.8 + - + +
51G ALA 4.5 5.1 + - - -
64G GLY* 4.7 1.2 - - - -
65G SER 4.9 0.6 + - - -
71G PHE* 4.1 9.6 - - + +
72G THR 4.0 4.8 - - - -
73G LEU* 3.4 61.8 - - + +
86G TYR 5.0 2.2 - - - -
87G TYR* 3.1 29.8 - - - -
88G CYS* 3.7 12.6 - - + -
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Residues in contact with TYR 36 (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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45D LEU* 6.2 0.7 - - + -
101D GLY 3.7 6.4 + - - -
102D ILE* 3.9 0.4 - - + +
103D GLY* 3.1 35.2 + - - -
106D TRP* 3.9 24.9 - + + -
34G GLY* 3.4 27.5 - - - -
35G TRP* 1.3 75.4 - - - +
37G GLN* 1.3 61.9 + - - +
44G PRO* 5.5 3.1 - - + -
45G LYS 3.3 7.4 - - - +
46G ARG* 3.1 37.6 + - + +
47G LEU* 4.2 3.1 - - - +
85G THR 3.6 0.9 - - - +
86G TYR* 3.1 11.7 - - - +
87G TYR* 2.8 55.1 + - + +
89G LEU* 3.4 33.4 - - + +
98G PHE* 4.5 9.2 - + + -
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Residues in contact with GLN 37 (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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36G TYR* 1.3 72.7 - - - +
38G GLN* 1.3 64.7 + - - +
39G LYS* 3.8 20.6 + - + +
43G ALA 4.8 0.2 - - - +
44G PRO* 3.3 5.1 - - - +
45G LYS* 2.7 66.7 + - + +
47G LEU* 3.4 20.5 - - + +
62G PHE* 4.1 14.1 - - - -
82G ASP* 4.3 10.3 + - - +
84G ALA* 3.6 19.4 - - + +
85G THR 3.8 2.2 - - - -
86G TYR* 2.9 35.3 + - + -
87G TYR* 5.6 0.2 - - - -
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Residues in contact with GLN 38 (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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39D GLN* 3.6 14.6 + - - +
45D LEU* 4.7 3.0 - - - +
94D TYR* 3.1 27.1 + - - -
37G GLN* 1.3 74.8 - - - +
39G LYS* 1.3 69.2 + - - +
42G LYS 4.7 5.0 + - - +
44G PRO* 3.7 25.5 - - + +
84G ALA* 3.2 7.1 - - - +
85G THR* 2.9 47.1 + - - +
87G TYR* 3.2 34.6 + - + -
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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