Contacts of the strand formed by residues 616 - 624 (chain A) in PDB entry 2VZ3
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 GLY 616 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A MET* 4.4 2.9 - - - -
234A ASP 4.2 13.9 - - - -
235A GLY* 4.6 5.2 + - - -
237A GLY 5.3 2.0 - - - -
575A ARG* 4.3 5.6 - - - -
614A LEU 3.5 0.8 + - - -
615A PRO* 1.3 75.1 - - - +
617A TYR* 1.3 65.4 + - - -
618A TRP* 3.3 7.9 - - - -
636A ARG* 3.7 5.5 - - - -
637A VAL 2.8 34.0 + - - -
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Residues in contact with TYR 617 (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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178A PRO* 3.5 40.4 - - + -
179A THR* 3.4 31.8 - - + +
233A MET* 3.5 16.7 - - - +
237A GLY* 3.7 32.2 + - - -
255A SER* 5.1 1.8 - - - -
256A SER* 4.9 7.3 + - - -
575A ARG* 3.5 9.0 - - - +
576A TYR* 3.1 27.9 + - + +
616A GLY* 1.3 72.8 - - - -
618A TRP* 1.3 60.5 + - - +
634A THR* 4.1 17.0 - - + -
635A ILE 3.6 1.3 - - - -
636A ARG* 3.6 44.0 + - + -
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Residues in contact with TRP 618 (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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573A LEU* 3.6 42.2 - - + -
574A ILE 3.4 5.2 - - - -
575A ARG* 3.2 39.6 - - - +
576A TYR* 3.5 11.9 - - - -
588A ARG* 3.6 28.7 - - + -
590A ILE* 3.4 31.6 - - + -
612A VAL 4.0 1.1 - - - -
613A ALA* 3.8 4.9 - - + -
614A LEU 2.9 42.0 + - - -
616A GLY 3.3 7.3 + - - -
617A TYR* 1.3 81.8 - - - +
619A MET* 1.3 59.5 + - - +
634A THR* 3.6 0.7 - - - -
635A ILE* 2.8 36.6 + - + +
637A VAL* 3.3 31.7 - - + +
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Residues in contact with MET 619 (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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501A LEU* 3.7 32.1 - - + +
502A LEU 4.0 4.5 - - - +
503A PRO* 3.8 19.7 - - - -
572A SER 3.5 1.4 - - - +
573A LEU* 3.2 7.6 - - - -
574A ILE* 2.7 54.0 + - + +
575A ARG 4.4 0.2 - - - +
576A TYR* 3.3 50.3 - - + +
577A GLY 5.2 1.1 - - - +
618A TRP* 1.3 72.7 - - - +
620A LEU* 1.3 60.4 + - - +
621A PHE* 3.5 33.2 + - + -
632A ALA* 3.5 8.3 - - + -
633A SER 3.7 4.0 - - - -
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Residues in contact with LEU 620 (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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546A ILE* 3.9 26.5 - - + +
549A THR* 4.8 3.4 - - + -
560A ILE* 5.4 0.9 - - + -
562A ILE* 4.1 25.6 - - + -
571A ALA* 4.7 0.4 - - + -
572A SER 3.5 2.7 - - - +
573A LEU* 3.8 11.0 - - + +
592A LEU* 3.6 31.2 - - + -
604A PHE* 4.0 17.3 - - + -
618A TRP 4.0 0.8 + - - -
619A MET* 1.3 72.1 - - - +
621A PHE* 1.3 70.3 + - - +
622A VAL* 4.5 6.1 - - + -
632A ALA* 3.3 4.7 - - - -
633A SER* 2.7 44.9 + - - +
635A ILE* 4.1 11.9 - - + -
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Residues in contact with PHE 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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448A PRO* 3.7 39.9 - - + -
501A LEU* 3.9 4.7 - - + -
502A LEU 4.1 7.4 - - - -
503A PRO 3.4 21.3 - - - -
505A GLY* 4.0 9.6 - - - -
571A ALA* 3.2 5.7 - - - +
572A SER* 2.9 36.0 + - - +
574A ILE* 3.7 24.5 - - + -
619A MET* 3.5 33.9 - - + -
620A LEU* 1.3 75.0 - - - +
622A VAL* 1.3 62.4 + - - +
623A MET* 4.0 7.6 - - - +
629A PRO* 4.4 2.0 - - + -
630A SER* 3.3 24.9 - - - +
632A ALA* 3.6 20.6 - - + -
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Residues in contact with VAL 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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544A PRO* 3.7 5.7 - - + +
546A ILE* 3.6 24.7 - - + +
562A ILE* 3.7 29.6 - - + -
564A THR* 4.2 3.8 - - + -
568A ILE* 3.6 31.9 - - + -
570A LYS 3.6 3.6 - - - -
571A ALA* 4.0 13.0 - - + -
620A LEU* 4.4 4.5 + - + -
621A PHE* 1.3 76.9 - - - +
623A MET* 1.3 62.3 + - - +
629A PRO* 3.2 1.6 - - - +
630A SER* 2.7 53.6 + - - +
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Residues in contact with MET 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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448A PRO* 3.7 28.5 - - + +
449A ASP* 4.6 11.2 - - + +
568A ILE* 3.6 6.0 - - - +
569A SER* 2.8 24.5 + - - -
570A LYS* 2.9 38.8 + - + +
571A ALA* 4.0 11.2 - - - +
572A SER* 3.8 10.3 - - - +
589A ARG* 6.1 0.7 - - - +
621A PHE* 4.0 12.1 - - - -
622A VAL* 1.3 81.5 - - - +
624A ASN* 1.3 64.7 + - - +
627A GLY* 4.0 14.6 - - - +
628A VAL 3.2 4.3 - - - +
629A PRO* 3.7 29.8 - - + -
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Residues in contact with ASN 624 (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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542A THR 4.0 7.5 + - - -
544A PRO* 3.5 31.2 - - + +
566A SER* 5.0 5.2 + - - +
567A SER 3.7 19.1 - - - +
568A ILE* 4.5 0.9 - - - +
569A SER* 3.9 8.4 - - - +
623A MET* 1.3 76.7 - - - +
625A SER* 1.3 59.5 + - - +
626A ALA* 2.8 20.9 + - - +
627A GLY* 2.8 32.1 + - - -
628A VAL* 3.0 23.8 + - - +
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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