Contacts of the strand formed by residues 119 - 124 (chain G) in PDB entry 3JZT
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 119 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56G ILE* 4.7 3.8 - - + -
61G PRO* 4.3 11.4 - - + +
62G ASP 4.2 9.9 - - - +
64G LEU* 4.0 35.9 - - + +
82G ILE* 6.2 0.4 - - + -
85G PHE* 4.3 24.5 - - + -
86G THR* 4.7 9.9 - - + -
114G ASN* 3.6 3.0 + - - -
115G VAL* 2.8 26.3 + - - +
116G LEU* 3.2 21.1 + - + -
117G GLU 2.8 11.3 + - - +
118G HIS* 1.3 75.2 - - - +
120G SER* 1.3 65.9 + - - +
121G VAL* 5.1 4.5 - - + -
100H SER* 3.4 28.3 - - - +
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Residues in contact with SER 120 (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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62G ASP 2.8 19.5 + - - -
63G VAL* 3.2 8.0 - - - -
64G LEU* 2.6 34.7 + - - +
111G LEU* 4.0 16.7 - - - +
112G PHE 3.5 6.3 - - - -
113G GLU* 3.0 12.9 + - - +
114G ASN* 2.7 23.5 + - - +
119G LEU* 1.3 74.8 - - - +
121G VAL* 1.3 56.9 + - - +
122G LEU 4.1 0.2 - - - -
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Residues in contact with VAL 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G LEU* 3.1 16.2 - - + +
66G ASN* 4.1 9.6 - - + -
82G ILE* 3.9 25.8 - - + -
86G THR* 5.4 2.0 - - + -
90G LEU* 3.9 17.3 - - + -
110G VAL 4.0 0.2 - - - +
111G LEU* 3.6 2.4 - - - +
112G PHE* 2.9 34.4 + - + +
115G VAL* 3.7 23.1 - - + +
119G LEU* 5.1 7.9 - - + +
120G SER* 1.3 77.3 - - - +
122G LEU* 1.3 65.7 + - - +
123G ASN* 3.9 21.4 + - - +
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Residues in contact with LEU 122 (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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63G VAL* 4.3 7.0 - - + -
64G LEU 2.7 11.1 + - - +
65G VAL* 3.6 17.4 - - + -
66G ASN* 2.6 34.3 + - - +
109G ALA* 3.7 25.4 - - + -
110G VAL 3.4 10.3 - - - +
111G LEU* 3.5 26.7 - - + -
120G SER 4.0 0.4 + - - -
121G VAL* 1.3 74.5 - - - +
123G ASN* 1.3 60.4 + - - +
124G ALA* 3.5 2.8 + - + -
144G ALA* 5.2 3.8 - - + +
145G ILE* 3.8 27.6 - - + -
148G CYS* 4.0 19.3 - - - -
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Residues in contact with ASN 123 (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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66G ASN* 3.3 24.2 + - - +
68G ALA* 4.8 2.7 - - + -
72G LEU* 4.8 15.6 - - + +
74G HIS* 3.9 10.4 - - - -
90G LEU* 4.1 1.6 - - - +
104G ILE* 4.1 18.1 - - + +
109G ALA* 3.0 5.8 - - - -
110G VAL* 2.6 35.8 + - - +
112G PHE* 3.5 47.7 - - - -
121G VAL* 3.9 12.4 + - - +
122G LEU* 1.3 70.5 - - - +
124G ALA* 1.3 62.4 + - - +
125G VAL* 3.8 1.2 + - + -
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Residues in contact with ALA 124 (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 VAL* 4.0 12.6 - - + -
66G ASN 2.8 16.6 + - - +
67G ALA* 3.4 2.8 - - - -
68G ALA 2.6 31.5 + - - +
109G ALA* 3.7 11.0 - - + -
122G LEU* 3.5 3.5 + - + -
123G ASN* 1.3 72.6 - - - +
125G VAL* 1.3 60.8 + - - +
126G GLY 3.7 2.6 + - - -
141G VAL* 3.6 24.7 - - + -
145G ILE* 4.9 0.4 - - + -
157G ILE* 3.9 16.6 - - + +
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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