Contacts of the strand formed by residues 375 - 379 (chain C) in PDB entry 1IR1
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 LEU 375 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C ILE* 3.8 28.6 - - + +
158C GLU* 3.7 33.0 - - + +
159C ARG* 5.3 7.9 - - + +
169C LEU* 4.2 11.4 - - + -
324C ASP 3.0 16.2 + - - +
325C HIS* 3.3 14.4 - - + +
326C ILE 3.1 22.3 + - - -
374C VAL* 1.3 70.9 - - - +
376C PRO* 1.3 67.2 - - - +
377C VAL* 3.7 1.2 - - - +
397C ASP* 3.5 38.1 - - + +
398C SER 3.7 4.3 - - - +
399C VAL* 4.1 15.5 - - + -
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Residues in contact with PRO 376 (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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326C ILE* 3.5 9.9 - - + +
328C SER* 3.6 21.3 - - - +
346C VAL* 4.2 17.5 - - + -
349C LEU* 4.9 6.5 - - + -
350C ARG* 3.6 20.9 - - + +
374C VAL 3.3 10.5 - - - +
375C LEU* 1.3 83.5 - - + +
377C VAL* 1.3 60.7 + - - +
378C ALA 4.1 0.4 - - - -
394C PHE* 4.5 4.9 - - + -
397C ASP 3.3 25.4 - - - +
398C SER* 3.3 8.8 - - - -
399C VAL 3.0 23.0 + - - -
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Residues in contact with VAL 377 (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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292C HIS* 3.9 8.1 - - + -
325C HIS* 3.7 30.7 - - + +
326C ILE 2.9 14.3 + - - +
327C HIS* 3.3 22.2 - - + +
328C SER* 3.0 25.7 + - - -
329C GLY 3.9 1.0 + - - -
375C LEU 3.7 2.2 - - - +
376C PRO* 1.3 79.4 - - - +
378C ALA* 1.3 62.1 + - - +
379C SER 3.7 2.4 + - - -
399C VAL* 3.3 22.2 - - + +
401C GLN* 3.4 38.8 - - + +
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Residues in contact with ALA 378 (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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328C SER* 4.7 0.2 - - - -
329C GLY 3.5 18.6 - - - +
330C THR* 3.8 8.3 - - + -
376C PRO 4.1 0.8 - - - -
377C VAL* 1.3 69.1 - - - +
379C SER* 1.3 62.1 - - - +
382C ILE* 3.7 4.5 - - + +
390C LEU* 4.3 6.1 - - + -
394C PHE* 3.8 20.6 - - + -
398C SER* 5.8 0.6 - - - -
399C VAL 2.8 8.3 + - - -
400C LEU* 3.5 24.3 - - + -
401C GLN* 2.9 25.8 + - - +
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Residues in contact with SER 379 (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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173C THR* 4.7 1.4 + - - -
327C HIS* 4.0 13.2 - - - -
329C GLY 4.4 1.7 + - - -
330C THR* 3.2 20.8 + - - +
335C LEU* 4.4 2.9 - - - +
377C VAL* 3.7 3.4 + - - -
378C ALA* 1.3 77.0 - - - +
380C GLY* 1.3 60.2 + - - +
382C ILE* 4.2 0.9 - - - -
401C GLN* 3.8 38.1 + - - +
501C CAP 2.8 52.3 + - - -
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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