Contacts of the strand formed by residues 324 - 328 (chain C) in PDB entry 1XFV
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 THR 324 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C ALA* 3.0 30.5 + - - +
322C LEU* 2.9 24.4 - - + +
323C ASN* 1.3 85.8 - - - +
325C TYR* 1.3 64.8 + - - +
326C ILE* 3.7 5.0 + - - +
497C LEU* 5.0 2.3 - - - +
498C ALA 2.9 17.0 - - - -
499C PRO* 3.2 24.5 - - + -
500C SER 4.1 0.2 - - - +
503C GLU* 4.6 4.0 - - + -
552C TRP* 5.3 1.7 - - - -
556C MET* 4.0 24.3 - - + +
598C PRO* 4.4 4.3 - - - +
624C TYR* 4.3 3.1 - - - -
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Residues in contact with TYR 325 (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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324C THR* 1.3 71.8 + - - +
326C ILE* 1.3 61.7 + - - +
327C LEU* 3.7 9.0 - - + +
497C LEU* 3.4 5.9 - - - +
498C ALA* 2.6 47.8 + - + -
595C ILE* 4.0 11.7 - - + -
596C ILE 3.8 5.2 - - - -
597C ASN* 3.9 20.6 - - + +
598C PRO* 3.1 29.2 - - + +
614C PHE* 3.9 19.7 - + - -
618C ASN* 3.2 29.0 + - + +
619C ILE* 3.8 22.9 - - + -
622C LYS* 5.8 0.9 - - - +
624C TYR* 3.5 38.2 - + - -
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Residues in contact with ILE 326 (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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315C PHE* 4.8 11.4 - - + -
319C ALA* 4.6 20.2 - - + +
324C THR* 3.9 11.0 - - - +
325C TYR* 1.3 75.7 - - - +
327C LEU* 1.3 65.1 + - - +
328C PHE* 3.2 31.9 - - + -
494C LEU* 3.5 18.8 - - + -
496C ALA 4.0 2.0 - - - -
497C LEU* 3.8 14.6 - - + -
556C MET* 4.7 5.6 - - - -
560C LEU* 3.7 30.5 - - + -
595C ILE* 3.3 4.7 - - - +
596C ILE* 2.9 41.5 + - + +
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Residues in contact with LEU 327 (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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325C TYR* 3.7 25.1 - - + +
326C ILE* 1.3 83.5 - - - +
328C PHE* 1.3 56.5 + - - +
494C LEU* 3.3 5.8 - - - +
495C PHE* 2.5 41.9 + - + -
496C ALA* 3.0 32.4 + - + +
498C ALA* 4.6 2.2 - - + +
593C ILE* 4.2 11.0 - - + -
594C PHE 3.3 7.9 - - - +
595C ILE* 3.7 28.3 - - + -
615C ILE* 4.1 18.2 - - + -
619C ILE* 4.0 19.1 - - + -
626C TYR* 5.0 0.7 - - + -
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Residues in contact with PHE 328 (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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307C LEU* 3.6 32.3 - - + -
315C PHE* 3.4 28.9 - + - -
326C ILE* 3.2 29.2 - - + -
327C LEU* 1.3 76.0 - - - +
329C ARG* 1.3 70.9 + - - +
331C VAL* 5.1 1.1 - - + -
492C TYR* 3.7 32.3 - - + -
493C ASP 3.6 10.1 - - - +
494C LEU* 3.4 18.6 - - + -
495C PHE* 4.1 2.0 - - - -
560C LEU* 4.6 3.1 - - + -
575C VAL* 4.8 3.1 - - + -
593C ILE* 3.4 9.9 - - - +
594C PHE* 2.9 41.5 + + + +
596C ILE* 4.0 14.1 - - + -
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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