Contacts of the strand formed by residues 602 - 606 (chain C) in PDB entry 1GGE
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 VAL 602 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C PRO* 5.4 9.0 - - + -
264C ARG* 4.8 4.7 - - - +
600C GLY 4.2 7.9 - - - +
601C ARG* 1.3 79.8 - - - +
603C VAL* 1.3 73.3 + - - +
629C HIS* 3.3 25.1 - - + +
630C ALA* 4.3 4.3 - - - +
631C LYS* 4.0 15.0 - - - -
661C THR 4.7 7.6 - - - +
662C VAL* 3.4 22.8 - - + +
663C ASP* 2.7 46.8 + - - +
664C ALA 3.5 0.7 + - - -
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Residues in contact with VAL 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602C VAL* 1.3 80.8 - - - +
604C ALA* 1.3 75.6 + - - +
605C ILE* 3.7 4.6 + - + -
623C LEU* 4.1 13.5 - - + -
628C VAL* 3.7 11.7 - - + -
629C HIS 2.8 12.3 + - - +
630C ALA* 3.2 4.7 - - - +
631C LYS 3.0 24.3 + - - -
664C ALA* 3.5 15.3 - - + +
666C ILE* 3.5 31.9 - - + -
732C LEU* 4.7 1.3 - - + -
736C MET* 3.6 34.3 - - + -
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Residues in contact with ALA 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603C VAL* 1.3 74.3 - - - +
605C ILE* 1.3 59.2 + - - +
606C LEU* 4.0 2.2 - - + -
631C LYS* 3.7 6.1 - - - -
633C LEU* 3.8 11.4 - - + -
662C VAL* 3.7 20.5 - - + +
664C ALA 3.0 8.3 + - - +
665C VAL* 3.4 3.1 - - + +
666C ILE 2.9 26.3 + - - +
684C TYR* 3.2 37.7 - - + +
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Residues in contact with ILE 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603C VAL* 4.4 13.0 - - + +
604C ALA* 1.3 75.9 - - - +
606C LEU* 1.3 63.2 + - - +
607C LEU* 3.4 7.2 + - + +
616C LEU* 4.1 13.7 - - + -
619C ILE* 3.8 17.7 - - + -
620C LEU* 3.6 31.2 - - + -
623C LEU* 4.3 2.2 - - + -
630C ALA* 3.8 15.5 - - + -
631C LYS 2.9 10.2 + - - +
632C LEU* 3.7 17.7 - - + -
633C LEU 3.0 24.3 + - - -
666C ILE* 3.2 17.0 - - + +
668C PRO* 3.9 22.7 - - + -
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Residues in contact with LEU 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604C ALA* 4.3 1.6 - - + -
605C ILE* 1.3 72.6 - - - +
607C LEU* 1.3 64.9 + - - +
608C ASN* 4.8 0.5 + - - -
633C LEU* 3.9 27.6 - - + -
654C PHE* 3.7 22.4 - - + -
665C VAL* 3.8 12.6 - - + -
666C ILE 3.0 11.6 + - - +
667C VAL* 3.9 21.0 - - + +
668C PRO* 3.2 21.4 - - - +
675C ILE* 4.2 8.8 - - + +
681C ALA* 4.5 8.7 - - + +
684C TYR* 4.0 26.7 - - + -
685C LEU* 3.7 32.1 - - + -
704C PHE* 6.2 1.3 - - + -
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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