Contacts of the strand formed by residues 619 - 623 (chain A) in PDB entry 4ZGA
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 GLU 619 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A THR* 4.5 4.3 - - + +
593A GLU* 3.1 35.7 + - - +
596A HIS* 4.4 8.2 - - + +
597A LEU* 3.8 21.1 - - + +
601A ARG* 5.0 2.1 - - - +
612A ILE* 3.4 21.8 - - + +
613A LEU 3.3 15.7 - - - +
614A TYR* 3.3 18.6 - - + -
615A HIS* 4.0 0.2 - - - -
618A PHE* 1.3 75.7 - - - +
620A SER* 1.3 63.5 + - - +
631A TRP* 3.7 18.7 - - + -
632A THR* 3.3 5.7 - - - +
633A SER 2.8 38.2 + - - +
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Residues in contact with SER 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ILE* 3.4 7.4 - - - +
613A LEU* 3.2 51.3 + - - +
615A HIS* 4.2 5.8 - - - -
618A PHE* 4.8 6.3 - - - -
619A GLU* 1.3 79.4 - - - +
621A GLY* 1.3 59.9 + - - +
622A TYR* 4.2 2.4 + - - +
629A PRO* 4.3 10.0 - - - +
631A TRP* 3.1 25.3 - - - -
632A THR* 4.0 10.5 - - - -
700A THR 5.2 1.4 + - - -
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Residues in contact with GLY 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A TYR* 4.2 10.5 - - - -
611A ASP 3.4 6.3 - - - -
612A ILE* 4.8 0.2 - - - -
620A SER* 1.3 73.7 - - - +
622A TYR* 1.3 59.2 + - - -
629A PRO* 3.9 0.4 - - - -
630A LEU* 2.7 38.6 + - - +
631A TRP* 2.7 35.2 + - - -
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Residues in contact with TYR 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A TYR* 3.1 4.9 - - - -
611A ASP* 2.8 45.2 + - + +
613A LEU* 3.8 25.4 - - + -
620A SER* 3.8 2.8 + - - +
621A GLY* 1.3 73.2 - - - +
623A SER* 1.3 70.7 + - - +
624A GLU* 3.7 5.0 + - + -
627A LEU* 3.2 41.1 + - - -
628A MET* 3.4 14.1 - - - -
629A PRO* 3.7 7.9 - - + -
659A VAL* 3.8 23.8 - - + -
663A PHE 2.4 32.5 + - - -
664A SER* 3.5 7.2 - - - -
665A GLN* 4.5 0.4 + - + -
699A VAL* 5.0 2.2 - - + -
700A THR* 3.9 30.5 - - + +
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Residues in contact with SER 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A TYR* 5.3 0.2 + - - -
608A THR* 5.1 3.9 + - - -
609A ARG 3.9 7.8 + - - -
610A TYR* 4.2 2.9 - - - -
621A GLY 3.5 1.0 + - - -
622A TYR* 1.3 76.0 - - - +
624A GLU* 1.3 54.8 + - - +
625A ILE* 3.1 7.3 + - - +
626A PHE* 2.9 34.0 + - - -
627A LEU* 2.8 32.9 + - - -
628A MET 2.8 20.6 + - - -
630A LEU* 3.5 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