Contacts of the strand formed by residues 472 - 480 (chain H) in PDB entry 4ZZ7
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 THR 472 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118H LEU* 3.9 20.0 - - + -
136H PHE* 3.4 38.6 - - + +
137H GLN 3.1 14.4 - - - +
139H MET* 3.7 7.4 - - - -
165H CYS* 4.1 10.1 - - + +
242H ARG* 2.7 25.3 + - - -
468H VAL* 2.8 22.7 + - - +
469H ARG* 2.9 18.7 + - - +
470H PHE 3.3 0.8 + - - -
471H TYR* 1.3 84.1 - - - +
473H LYS* 1.3 59.0 + - - +
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Residues in contact with LYS 473 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430G GLN* 3.2 22.4 + - - -
452G TRP* 3.5 52.2 - - + +
453G LYS* 6.0 3.2 - - - +
461G HIS* 5.6 1.6 - - - +
57H ARG* 6.2 0.7 - - - +
135H GLU 3.4 0.4 - - - +
136H PHE* 4.4 3.1 - - - -
137H GLN 2.9 38.9 + - - +
138H PRO 3.3 20.0 - - - +
139H MET* 3.7 36.4 + - + +
218H LYS* 5.6 5.1 - - - +
242H ARG* 3.8 11.2 - - - +
469H ARG* 5.3 0.2 - - - +
472H THR* 1.3 75.9 - - - +
474H ARG* 1.3 63.2 + - - +
475H LYS 3.4 1.7 + - - -
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Residues in contact with ARG 474 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432G GLY* 3.7 4.7 - - - +
447G HIS* 4.6 5.7 + - - -
448G SER* 3.6 30.7 - - - +
450G GLY 4.6 0.3 - - - +
452G TRP* 3.0 18.2 + - - -
461G HIS* 3.5 32.8 + - + +
465G PRO* 4.2 19.3 - - - +
466G ASP* 2.6 35.8 + - - +
121H GLU* 5.1 4.6 + - - -
134H SER* 3.5 25.0 + - - -
135H GLU 3.5 5.4 - - - +
136H PHE* 3.8 30.0 - - + -
469H ARG* 3.7 13.9 - - - +
473H LYS* 1.3 71.2 - - - +
475H LYS* 1.3 63.9 + - - +
476H THR* 3.8 18.5 + - - +
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Residues in contact with LYS 475 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426G SER 2.7 29.7 + - - +
427G ASP 3.2 8.5 + - - -
429G ILE* 2.7 29.6 + - - +
430G GLN* 5.4 0.2 - - - +
431G VAL 3.4 13.0 - - - -
432G GLY 3.2 11.4 - - - +
434G VAL* 3.9 15.7 - - + -
452G TRP* 3.7 12.3 - - + -
133H TRP 4.0 0.2 - - - +
134H SER* 3.2 4.9 - - - -
135H GLU* 2.8 47.1 + - + +
137H GLN* 3.1 31.5 + - - +
473H LYS 3.4 0.8 + - - -
474H ARG* 1.3 73.4 - - - +
476H THR* 1.3 68.3 + - - +
477H VAL* 4.1 12.3 + - + -
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Residues in contact with THR 476 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432G GLY 3.0 9.5 + - - -
433G MET* 3.6 6.4 - - - +
434G VAL 3.1 22.7 + - - +
441G PRO 4.9 1.6 - - - +
443G PRO* 3.8 33.2 - - + -
447G HIS* 4.3 14.6 - - + +
448G SER 3.6 16.5 + - - -
132H SER* 3.8 18.8 - - - +
133H TRP 3.5 6.7 - - - +
134H SER* 4.4 1.1 - - - +
474H ARG* 3.8 15.6 + - - +
475H LYS* 1.3 75.2 + - - +
477H VAL* 1.3 62.3 + - - +
478H THR* 3.9 3.5 + - - +
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Residues in contact with VAL 477 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426G SER* 4.0 25.1 - - - +
434G VAL* 3.3 11.9 - - + +
436G ILE* 4.2 18.8 - - + -
132H SER* 2.6 25.6 + - - -
133H TRP* 2.9 70.2 + - + +
135H GLU* 5.1 5.8 - - + -
475H LYS* 4.4 17.5 - - + -
476H THR* 1.3 74.3 - - - +
478H THR* 1.3 60.2 + - - +
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Residues in contact with THR 478 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434G VAL 2.9 8.5 + - - -
435G GLY* 3.5 3.3 - - - -
436G ILE 3.0 23.1 + - - -
438G ILE* 3.8 19.2 - - + +
441G PRO* 4.1 29.1 + - + +
442G VAL 4.4 7.9 + - - +
443G PRO* 5.0 1.2 - - - +
126H VAL* 4.6 4.7 - - + -
130H ILE* 3.7 25.6 - - + -
131H ASP 3.7 4.9 - - - +
132H SER* 3.4 15.7 + - - -
476H THR* 4.7 5.0 + - - +
477H VAL* 1.3 73.3 - - - +
479H GLN* 1.3 61.1 + - - +
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Residues in contact with GLN 479 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E TRP* 6.0 1.7 - - - -
479E GLN* 5.2 13.8 + - - +
481E TRP* 6.3 0.4 - - - -
423F ARG* 4.8 12.1 - - - +
422G ALA* 5.0 4.8 - - - +
436G ILE* 3.8 24.5 - - + +
130H ILE* 3.5 5.4 - - - +
131H ASP* 2.8 39.7 + - + +
133H TRP* 3.5 36.0 - - + -
477H VAL 4.2 0.2 - - - -
478H THR* 1.3 73.2 - - - +
480H ARG* 1.3 65.9 + - - +
481H TRP* 3.5 40.8 + - + +
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Residues in contact with ARG 480 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423F ARG* 6.2 0.4 - - - +
263G ASN* 3.8 15.4 + - - +
267G GLN* 3.7 31.5 + - - +
436G ILE* 2.9 14.5 + - - +
437G ASN* 3.0 26.4 + - - +
438G ILE* 3.6 28.9 - - + -
128H PRO 5.4 1.8 + - - -
129H GLY 4.1 13.0 - - - +
130H ILE* 3.9 19.2 - - + +
479H GLN* 1.3 77.3 - - - +
481H TRP* 1.3 76.4 + - - +
482H PRO* 3.8 23.4 - - + +
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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