Contacts of the strand formed by residues 396 - 403 (chain A) in PDB entry 3I7K
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 ILE 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A GLY* 1.3 79.3 - - - +
397A HIS* 1.3 66.0 + - - +
398A GLU* 3.8 16.8 + - + +
650A PHE* 6.0 2.7 - - + -
671A VAL* 4.9 10.3 - - + -
672A ASN 5.3 1.0 + - - +
673A LEU* 3.2 47.8 - - + +
691A LEU* 5.4 4.9 - - + -
693A LEU* 4.8 16.4 - - + -
700A THR* 5.3 9.2 - - + -
701A ILE 6.2 0.4 - - - -
702A GLY* 5.6 6.5 - - - +
703A THR 3.1 18.8 - - - +
704A ILE* 3.6 22.2 - - + -
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Residues in contact with HIS 397 (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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368A GLU* 6.4 3.4 - - + -
391A ARG* 6.0 3.8 + - - -
396A ILE* 1.3 76.0 - - - +
398A GLU* 1.3 59.8 + - - +
399A HIS* 3.3 17.5 + - + +
702A GLY* 3.3 19.6 - - - -
703A THR* 3.4 23.5 + - - +
705A ASP* 4.1 19.1 + - - -
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Residues in contact with GLU 398 (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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396A ILE* 3.8 15.0 + - + +
397A HIS* 1.3 69.1 - - - +
399A HIS* 1.3 66.2 + - - +
400A ALA 5.1 1.6 - - - +
401A SER* 3.9 20.7 + - - -
673A LEU* 4.7 13.6 - - + +
700A THR* 3.8 25.9 + - + +
701A ILE 4.3 4.3 - - - -
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Residues in contact with HIS 399 (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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397A HIS* 3.5 16.5 + - + +
398A GLU* 1.3 75.0 - - - +
400A ALA* 1.3 60.5 + - - +
441A GLU* 5.3 3.1 - - - +
687A TYR* 4.0 26.7 - - + +
688A PRO* 5.5 2.9 - - + -
690A SER* 5.0 4.9 + - - -
701A ILE 3.2 10.2 + - - +
702A GLY* 3.5 22.8 + - - -
703A THR* 3.7 28.2 + - + +
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Residues in contact with ALA 400 (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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398A GLU* 5.2 1.1 - - - -
399A HIS* 1.3 80.6 - - - +
401A SER* 1.3 61.7 + - - +
402A ILE* 4.1 11.4 - - + -
687A TYR* 3.2 34.1 - - + +
700A THR* 3.4 22.2 - - - +
701A ILE* 3.5 24.5 + - + +
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Residues in contact with SER 401 (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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398A GLU* 3.9 20.3 + - - -
400A ALA* 1.3 76.1 - - - +
402A ILE* 1.3 62.7 + - - +
403A ASP* 3.9 2.8 + - - +
698A THR* 3.3 24.3 - - - +
699A LEU 3.5 5.4 + - - -
700A THR* 4.2 2.8 + - - -
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Residues in contact with ILE 402 (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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400A ALA* 4.4 17.3 - - + -
401A SER* 1.3 74.1 - - - +
403A ASP* 1.3 73.2 + - - +
404A LEU* 4.9 13.5 - - + -
436A LEU* 6.3 1.6 - - + -
443A VAL* 3.8 38.8 - - + +
445A GLU* 6.0 2.2 - - - +
687A TYR* 5.4 0.2 - - - +
698A THR* 4.4 0.9 - - - -
699A LEU* 2.8 47.0 + - + +
701A ILE* 4.6 11.2 - - + -
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Residues in contact with ASP 403 (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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401A SER 3.9 4.2 + - - +
402A ILE* 1.3 78.2 - - - +
404A LEU* 1.3 75.5 + - - +
405A PRO* 4.4 4.2 - - + +
697A SER 3.6 15.5 - - - +
698A THR* 4.1 9.6 - - + +
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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