Contacts of the strand formed by residues 477 - 483 (chain C) in PDB entry 1XMI
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 PRO 477 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397C VAL* 3.9 24.9 - - + -
398C THR 3.5 5.4 - - - +
399C ALA* 4.1 4.3 - - + -
410C GLU* 5.0 4.0 - - - +
470C MET* 4.2 2.7 - - + +
475C LEU 4.1 4.7 - - - +
476C GLU* 1.3 90.7 - - + +
478C SER* 1.3 62.1 + - - +
479C GLU 4.0 8.3 - - - +
480C GLY 5.4 4.3 - - - +
482C ILE* 3.8 23.3 - - + -
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Residues in contact with SER 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C THR 2.8 11.8 + - - -
399C ALA* 4.3 0.2 - - - +
400C PHE* 3.8 13.9 + - - -
406C GLY* 3.2 33.5 + - - -
409C PHE* 3.8 24.7 - - - -
410C GLU* 3.4 30.6 + - - +
476C GLU 3.7 2.6 + - - -
477C PRO* 1.3 73.9 - - - +
479C GLU* 1.3 61.6 + - - +
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Residues in contact with GLU 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C ASN* 3.7 12.9 - - + +
397C VAL* 3.2 24.9 - - - +
398C THR* 3.3 17.4 + - - +
409C PHE* 4.0 31.2 - - + -
413C LYS* 4.9 9.9 - - - +
477C PRO* 3.4 5.4 - - - +
478C SER* 1.3 82.2 - - - +
480C GLY* 1.3 65.6 + - - +
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Residues in contact with GLY 480 (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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395C GLU 3.3 13.9 - - - -
396C ASN* 3.3 7.9 - - - -
397C VAL* 4.3 2.2 - - - -
477C PRO* 5.4 5.5 - - - +
479C GLU* 1.3 81.8 - - - +
481C LYS* 1.3 75.7 + - - +
482C ILE* 4.1 1.1 + - - -
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Residues in contact with LYS 481 (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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393C VAL* 3.7 1.8 - - + +
394C MET* 3.3 5.5 - - - -
395C GLU* 2.9 59.0 + - + +
397C VAL* 3.4 2.6 - - - +
480C GLY* 1.3 86.2 + - - +
482C ILE* 1.3 62.8 + - - +
483C LYS* 4.1 26.2 - - + +
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Residues in contact with ILE 482 (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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392C VAL* 5.8 1.1 - - + -
393C VAL 3.4 4.9 - - - +
394C MET* 3.9 20.9 - - + -
397C VAL* 3.8 12.8 - - + -
470C MET* 3.8 32.3 - - + +
471C ILE* 5.7 0.7 - - - -
477C PRO* 3.8 31.9 - - + -
480C GLY 4.1 1.6 + - - +
481C LYS* 1.3 79.3 - - - +
483C LYS* 1.3 71.2 + - - +
484C HIS* 3.5 31.5 + - + +
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Residues in contact with LYS 483 (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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391C GLU* 3.5 2.6 - - + +
392C VAL* 3.3 4.0 - - - +
393C VAL* 2.8 58.5 + - + +
481C LYS* 4.1 27.4 - - + +
482C ILE* 1.3 77.4 - - - +
484C HIS* 1.3 66.6 + - - +
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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