Contacts of the strand formed by residues 621 - 626 (chain A) in PDB entry 1EUT
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 TYR 621 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A ALA* 3.6 23.3 - - + -
556A LEU 3.0 7.4 - - - +
557A ASP* 3.5 35.7 + - + -
558A LEU* 4.3 2.9 - - - -
587A THR* 3.5 6.1 - - - -
588A SER 3.0 29.4 + - - +
589A LEU 4.2 1.1 - - - -
590A ASN 4.0 7.2 + - - -
591A GLY* 3.3 40.9 - - - -
594A TRP* 3.3 20.0 - + + -
619A ALA* 3.8 4.4 - - - +
620A ARG* 1.3 122.6 + - + +
622A ILE* 1.3 63.3 + - - +
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Residues in contact with ILE 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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554A ILE 4.1 0.5 - - - +
555A SER* 3.2 1.4 - - - -
556A LEU* 2.8 44.6 + - + +
558A LEU* 3.6 21.8 - - + -
564A ILE* 4.5 19.5 - - + -
566A GLY 4.7 3.6 - - - +
567A LEU* 3.9 32.8 - - + -
585A ILE* 3.9 26.9 - - + -
586A TYR 3.7 4.7 - - - +
587A THR* 4.4 4.0 - - + -
594A TRP* 3.5 2.2 - - - -
614A PHE* 4.5 7.9 - - + -
621A TYR* 1.3 76.3 - - - +
623A ARG* 1.3 67.0 + - - +
641A LEU* 6.0 0.7 - - + -
643A VAL* 4.0 15.0 - - + -
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Residues in contact with ARG 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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513A ASP* 3.1 28.1 + - - -
553A ARG* 3.6 22.6 - - - +
554A ILE 3.4 4.7 - - - +
555A SER* 3.2 14.0 + - - +
585A ILE* 3.5 9.4 - - - +
586A TYR* 2.8 45.9 + - + +
594A TRP* 3.2 59.7 - - + +
622A ILE* 1.3 76.9 - - - +
624A LEU* 1.3 63.7 + - - +
625A VAL* 3.8 28.0 - - + -
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Residues in contact with LEU 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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538A TRP* 5.8 1.6 - - + -
553A ARG* 3.2 4.3 - - - +
554A ILE* 2.9 46.9 + - + +
567A LEU* 4.1 15.0 - - + -
569A TYR* 3.4 43.5 - - + -
580A VAL* 5.3 5.4 - - + -
583A TYR* 3.8 28.3 - - + -
584A GLU 3.9 3.4 - - - +
585A ILE* 4.4 4.3 - - + -
603A PHE* 4.7 4.5 - - + -
623A ARG* 1.3 72.8 - - - +
625A VAL* 1.3 64.5 + - - +
626A ALA* 4.9 3.5 - - + +
638A VAL* 5.0 11.0 - - + -
641A LEU* 4.1 17.9 - - + +
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Residues in contact with VAL 625 (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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551A PRO* 5.9 3.1 - - + -
552A HIS 3.6 7.9 - - - +
553A ARG* 4.0 11.9 - - + -
583A TYR* 3.2 8.1 - - - +
584A GLU* 3.0 41.0 + - + +
586A TYR* 3.8 18.6 - - + -
623A ARG* 3.8 28.3 - - + -
624A LEU* 1.3 73.8 - - - +
626A ALA* 1.3 59.8 + - - +
627A LEU* 3.5 28.5 - - + -
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Residues in contact with ALA 626 (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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538A TRP* 5.9 3.4 - - + -
550A TYR* 2.8 35.9 - - + +
551A PRO* 3.7 2.3 - - - +
552A HIS* 2.8 26.9 + - + +
553A ARG* 5.6 0.4 - - - -
580A VAL* 3.6 32.3 - - + -
582A ASP 3.6 4.3 - - - -
583A TYR* 4.6 0.2 - - - -
624A LEU* 4.0 6.3 + - + +
625A VAL* 1.3 72.7 - - - +
627A LEU* 1.3 61.9 + - - +
628A SER 3.6 0.2 - - - -
636A ALA* 4.8 2.9 - - + -
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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