Contacts of the strand formed by residues 559 - 564 (chain A) in PDB entry 1GOG
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 ARG 559 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A SER* 4.5 2.1 + - - -
551A THR* 4.4 6.8 - - - +
554A VAL* 4.0 4.2 - - - +
557A GLY 4.6 1.3 + - - -
558A GLY* 1.3 68.5 - - - +
560A ILE* 1.3 70.2 + - - +
561A THR* 5.4 1.8 - - - +
603A SER* 5.6 4.3 - - - -
604A PHE 3.4 6.1 - - - +
605A GLN* 3.4 51.9 + - + +
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Residues in contact with ILE 560 (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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549A THR* 4.7 3.6 - - + -
550A SER* 3.7 9.4 - - - +
551A THR* 4.0 24.5 - - + +
554A VAL* 3.6 32.1 - - + -
559A ARG* 1.3 79.7 - - - +
561A THR* 1.4 77.6 + - - +
562A ILE* 4.0 14.8 - - + -
573A LEU* 6.1 0.2 - - + -
603A SER* 3.0 5.8 - - - -
604A PHE* 3.0 62.7 + - + -
606A VAL* 4.5 2.9 - - + -
620A LEU* 5.5 0.2 - - + -
635A ILE* 3.8 25.8 - - + -
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Residues in contact with THR 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ARG* 4.4 0.3 - - - +
549A THR* 3.5 0.2 - - - -
550A SER* 2.8 46.0 + - - -
559A ARG* 5.4 1.7 - - - +
560A ILE* 1.4 74.5 - - - +
562A ILE* 1.3 72.2 + - - +
597A ASN* 3.8 10.8 - - - +
601A SER* 3.9 11.9 - - - +
602A TYR 3.2 10.8 - - - +
603A SER* 3.0 18.6 + - - +
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Residues in contact with ILE 562 (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* 4.3 6.1 - - + -
548A ARG 3.0 14.4 - - - +
549A THR* 3.9 17.7 - - + -
560A ILE* 4.0 11.7 - - + -
561A THR* 1.3 83.4 - - - +
563A SER* 1.3 63.6 - - - +
564A THR* 3.7 25.4 - - + -
568A ILE* 3.9 10.5 - - + -
594A LEU* 5.1 2.2 - - + -
601A SER* 3.3 4.4 + - - -
602A TYR* 2.6 51.7 + - + +
604A PHE* 4.2 13.7 - - + -
620A LEU* 4.1 12.8 - - + -
622A VAL* 3.8 23.6 - - + -
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Residues in contact with SER 563 (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* 3.7 2.4 - - - +
547A THR* 2.9 37.4 + - - -
548A ARG* 2.9 28.0 + - - +
562A ILE* 1.3 77.1 - - - +
564A THR* 1.3 67.8 + - - +
599A GLY 5.7 0.9 - - - -
600A ASN 3.2 10.1 - - - -
601A SER* 4.3 6.3 - - - +
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Residues in contact with THR 564 (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* 5.5 0.2 - - - -
545A LYS 3.1 15.9 - - - +
546A ILE* 4.6 2.9 - - - -
547A THR* 3.9 9.3 + - - +
562A ILE* 3.7 25.4 - - + -
563A SER* 1.3 82.6 - - - +
565A ASP* 1.3 61.8 - - - +
566A SER 2.5 25.9 + - - -
568A ILE* 4.2 21.5 - - + -
599A GLY 5.1 0.2 - - - +
600A ASN* 3.0 23.7 + - - +
602A TYR* 3.6 9.9 - - + -
622A VAL* 4.3 7.2 - - + -
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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