Contacts of the strand formed by residues 120 - 126 (chain G) in PDB entry 1RZK
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 120 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118G PRO* 3.2 6.3 - - - +
119G CYS* 1.3 79.5 - - - +
121G LYS* 1.3 64.1 + - - +
122G LEU* 3.4 28.5 - - + -
200G VAL* 3.6 17.7 - - + -
201G ILE 3.0 9.0 - - - +
202G THR* 4.4 3.8 - - - +
433G ALA* 3.3 2.3 - - - -
434G MET* 2.8 67.0 + - + -
52H ILE* 4.9 3.1 - - + -
54H LEU* 3.5 12.6 - - + -
56H VAL* 4.1 11.2 - - + -
58H HIS* 5.2 0.7 - - + +
94L TRP* 5.1 2.9 - - + -
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Residues in contact with LYS 121 (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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113G ASP* 4.9 11.7 + - - -
118G PRO* 4.6 15.5 - - + -
120G VAL* 1.3 75.7 - - - +
122G LEU* 1.3 65.2 + - - +
123G THR* 3.9 10.1 - - + +
199G SER 3.2 6.6 - - - +
200G VAL* 3.5 1.2 - - - -
201G ILE* 2.9 49.8 + - + +
203G GLN* 5.0 7.0 - - - +
426G MET* 3.1 39.0 - - + +
428G GLN* 5.5 0.2 - - - +
429G GLU* 2.7 40.1 + - - -
432G LYS 3.6 4.5 - - - -
433G ALA* 4.3 0.2 - - - +
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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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120G VAL* 3.4 31.2 - - + -
121G LYS* 1.3 75.1 - - - +
123G THR* 1.3 64.4 + - - +
198G THR* 3.5 19.7 - - + -
199G SER 3.4 3.8 - - - -
200G VAL* 3.8 8.7 - - + -
431G GLY* 3.0 23.8 - - - -
432G LYS* 2.9 36.7 + - + +
433G ALA* 5.8 0.2 - - - -
54H LEU* 3.7 38.1 - - + +
56H VAL* 3.4 20.4 - - + -
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Residues in contact with THR 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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63C ASP* 6.0 0.9 - - - +
121G LYS* 3.9 18.4 + - - +
122G LEU* 1.3 81.9 - - - +
124G PRO* 1.3 75.9 - - - +
198G THR* 3.9 4.9 - - - +
199G SER* 2.9 46.6 + - - -
201G ILE* 5.3 4.7 - - - +
426G MET* 5.0 0.4 - - - -
429G GLU* 3.3 28.9 - - + +
430G VAL 3.3 16.2 - - - +
431G GLY* 4.4 0.9 - - - -
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Residues in contact with PRO 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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59C ARG* 5.2 0.2 - - + -
60C SER* 3.2 51.6 - - - +
63C ASP* 4.5 15.6 - - + +
64C GLN* 5.5 1.7 + - - -
123G THR* 1.3 90.9 - - - +
125G LEU* 1.3 60.2 - - - +
126G CYS* 4.2 0.7 - - - -
196G CYS* 5.5 0.2 - - + -
197G ASN 4.1 4.0 - - - +
198G THR* 5.0 3.6 - - - +
199G SER* 5.3 0.3 - - - -
430G VAL* 3.3 36.3 - - + +
431G GLY* 4.2 3.4 - - - -
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Residues in contact with LEU 125 (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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64C GLN* 5.0 0.4 - - - +
123G THR 4.2 4.0 - - - +
124G PRO* 1.3 76.9 - - - +
126G CYS* 1.3 64.5 + - - +
127G VAL* 5.9 0.3 - - - +
195G SER 4.6 0.2 - - - +
196G CYS* 3.7 0.2 - - - -
197G ASN* 3.0 42.4 + - + +
198G THR 5.3 0.2 - - - -
199G SER* 4.4 20.4 - - - +
697G NAG 3.5 40.4 - - - +
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Residues in contact with CYS 126 (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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60C SER* 3.6 18.4 - - - -
61C LEU* 3.8 8.1 - - + -
64C GLN* 3.1 36.7 + - + +
125G LEU* 1.3 77.5 - - - +
127G VAL* 1.3 64.1 + - - +
128G GLY* 3.8 7.6 - - - +
194G GLY 4.5 0.9 - - - +
195G SER 3.8 7.9 - - - +
196G CYS* 2.0 48.0 - - - -
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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