Contacts of the helix formed by residues 558 - 564 (chain A) in PDB entry 2FGJ
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 SER 558 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557A ARG* 1.3 79.1 - - - +
559A ILE* 1.3 63.5 + - - +
560A ILE* 3.1 2.5 - - - +
561A ASP* 3.1 18.4 + - - +
562A ASN* 3.0 26.0 + - - +
595A TYR 3.7 10.8 - - - -
596A ASN* 3.8 15.5 - - - -
598A ILE* 3.3 19.9 - - - +
558D SER* 5.5 1.8 - - - -
561D ASP* 2.7 29.0 + - - -
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Residues in contact with ILE 559 (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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557A ARG 3.8 0.2 + - - -
558A SER* 1.3 69.2 - - - +
560A ILE* 1.3 66.8 + - - +
562A ASN* 2.9 8.7 + - - +
563A ILE* 2.9 37.6 + - + +
587A PHE* 5.3 0.4 - - + -
588A ILE* 4.1 19.5 - - + -
591A LEU* 3.9 20.6 - - + -
594A GLY 3.9 19.3 - - - +
595A TYR* 3.0 15.4 + - + +
597A THR* 4.1 8.5 - - + -
598A ILE 4.1 1.0 - - - +
599A VAL* 3.8 26.9 - - + -
606A LEU* 5.0 4.5 - - + -
614A ILE* 3.7 31.0 - - + -
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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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558A SER* 3.1 20.6 - - - +
559A ILE* 1.3 75.7 - - - +
561A ASP* 1.3 57.6 + - - +
563A ILE* 3.5 1.9 + - - +
564A SER* 2.9 35.7 + - - +
572A VAL* 4.4 14.8 - - + -
575A VAL* 3.3 44.2 - - + -
595A TYR* 2.8 28.8 + - + +
596A ASN* 3.6 16.2 - - - +
557D ARG* 3.5 41.5 - - - +
561D ASP* 3.5 12.3 - - - +
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Residues in contact with ASP 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A LEU* 5.2 2.6 - - - +
557A ARG* 3.0 26.7 + - - -
558A SER* 3.1 23.3 + - - +
560A ILE* 1.3 74.8 - - - +
562A ASN* 1.3 65.1 + - - +
564A SER* 3.5 5.2 + - - -
565A LEU* 3.5 18.5 + - - +
557D ARG* 6.3 0.2 - - - +
561D ASP* 3.3 25.6 - - - +
564D SER* 4.5 6.4 - - - +
568D PRO* 3.0 45.3 - - - +
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Residues in contact with ASN 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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554A LEU* 3.5 28.5 - - + +
555A LEU* 2.9 56.8 - - - +
557A ARG* 3.5 5.3 - - - +
558A SER 3.0 19.2 + - - +
559A ILE* 2.9 11.7 + - - +
561A ASP* 1.3 74.0 - - - +
563A ILE* 1.3 65.0 + - - +
565A LEU* 3.2 29.7 - - - +
599A VAL* 3.3 7.6 - - - +
614A ILE* 4.7 3.1 - - + -
618A ARG* 3.3 14.8 + - - +
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Residues in contact with ILE 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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559A ILE* 2.9 36.7 + - + +
560A ILE 4.0 3.4 - - - +
562A ASN* 1.3 72.8 - - - +
564A SER* 1.3 58.1 + - - +
565A LEU 3.1 5.3 + - - -
566A ALA* 3.4 15.8 + - - +
570A MET* 4.8 0.7 - - + -
575A VAL* 3.8 34.3 - - + +
578A ALA* 5.0 1.1 - - + -
579A ALA* 4.8 5.6 - - + -
595A TYR* 4.5 6.7 - - + -
614A ILE* 4.0 28.0 - - + +
617A ALA* 4.1 16.8 - - + -
618A ARG* 3.6 20.1 - - - +
621A VAL* 3.8 26.3 - - + +
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Residues in contact with SER 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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560A ILE* 2.9 26.7 + - - +
561A ASP* 3.9 7.6 - - - -
562A ASN 3.3 0.8 - - - -
563A ILE* 1.3 72.2 - - - +
565A LEU* 1.3 62.5 + - - +
566A ALA 3.0 3.4 + - - +
567A ASN 3.2 4.2 + - - -
568A PRO* 3.2 26.9 - - - +
569A GLY 5.3 1.3 - - - -
570A MET* 3.8 33.3 + - - +
575A VAL* 4.0 7.8 - - - +
557D ARG* 5.1 4.1 + - - -
565D LEU* 6.6 0.7 - - - -
568D PRO* 3.5 11.7 - - - +
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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