Contacts of the strand formed by residues 411 - 421 (chain F) in PDB entry 5IG3
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 HIS 411 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A ASP* 3.1 44.6 + - + +
394A PHE 4.2 0.2 - - - -
396A ARG* 6.2 1.3 - - - -
397A PHE* 3.8 20.7 + + + +
410F VAL* 1.3 77.5 - - - +
412F THR* 1.3 81.0 + - - +
413F THR* 4.0 13.5 + - - -
434F ILE 3.8 0.7 - - - +
435F THR* 3.4 4.1 - - - -
436F GLN* 2.9 57.3 + - - +
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Residues in contact with THR 412 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358F ILE* 4.9 15.0 - - + +
362F SER* 5.2 5.4 + - - -
410F VAL* 4.9 8.0 - - - +
411F HIS* 1.3 85.7 + - - +
413F THR* 1.3 69.6 + - - +
414F ILE* 4.6 9.0 - - + -
433F ARG* 3.6 36.1 + - + -
434F ILE 3.4 4.0 - - - +
435F THR* 4.1 11.2 + - - +
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Residues in contact with THR 413 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A VAL* 5.3 4.0 - - + -
394A PHE* 4.2 21.3 + - + +
411F HIS* 4.0 18.6 + - - -
412F THR* 1.3 76.3 + - - +
414F ILE* 1.3 65.8 + - - +
415F LEU* 3.9 24.4 + - + -
432F ILE 3.7 1.4 - - - +
433F ARG* 3.7 1.0 - - - -
434F ILE* 2.9 45.7 + - + +
436F GLN* 4.7 1.4 + - - -
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Residues in contact with ILE 414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354F THR* 5.4 6.7 - - + -
355F GLU* 6.0 6.5 - - + -
358F ILE* 5.0 15.7 - - + -
412F THR* 4.6 13.9 - - + -
413F THR* 1.3 77.9 - - - +
415F LEU* 1.3 67.1 + - - +
416F ASN 4.4 0.5 + - - -
417F PRO* 3.7 20.2 - - + +
429F ILE* 6.4 0.2 - - + -
431F TYR* 3.7 49.4 - - + -
432F ILE 3.4 3.4 - - - +
433F ARG* 4.9 3.4 - - + -
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Residues in contact with LEU 415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A ASN* 3.6 36.3 - - + +
388A LEU 4.3 15.3 - - - +
389A VAL* 4.6 15.3 - - + -
390A GLU 5.5 1.8 - - - +
413F THR* 4.0 17.7 - - + -
414F ILE* 1.3 80.2 - - - +
416F ASN* 1.3 80.4 + - - +
417F PRO 3.4 3.2 - - - -
431F TYR* 4.0 0.7 - - - -
432F ILE* 2.8 42.8 + - + +
434F ILE* 3.7 26.9 - - + -
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Residues in contact with ASN 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A ASN* 5.1 5.7 - - - +
415F LEU* 1.3 84.4 - - - +
417F PRO* 1.3 73.0 - - - +
418F HIS* 3.3 6.1 + - - +
430F ALA 3.8 5.2 - - - +
431F TYR* 4.2 2.3 - - - -
432F ILE* 4.5 15.6 + - + +
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Residues in contact with PRO 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351F ILE* 4.8 19.5 - - + -
414F ILE* 3.7 26.2 - - + +
415F LEU* 3.4 1.8 - - - -
416F ASN* 1.3 88.0 - - - +
418F HIS* 1.3 59.5 + - - +
419F ILE* 4.3 3.7 - - + +
429F ILE* 4.8 6.3 - - + -
430F ALA 3.6 7.4 - - - +
431F TYR* 4.0 9.9 - - + -
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Residues in contact with HIS 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347F LYS* 6.3 0.2 - - - -
416F ASN 3.3 3.8 + - - +
417F PRO* 1.3 74.1 - - - +
419F ILE* 1.3 76.5 + - - +
420F HIS* 3.4 39.7 + + + +
428F CYS 4.0 0.7 - - - +
429F ILE* 3.4 2.8 - - - +
430F ALA* 2.9 42.0 + - + +
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Residues in contact with ILE 419 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347F LYS* 3.5 63.7 + - + +
350F ILE* 4.5 18.6 - - + -
351F ILE* 3.8 21.8 - - + -
417F PRO* 5.1 3.1 - - + +
418F HIS* 1.3 93.1 + - - +
420F HIS* 1.3 67.1 + - - +
421F LEU* 3.9 26.3 + - + -
427F ALA* 5.0 0.9 - - + -
428F CYS 3.7 7.2 - - - +
429F ILE* 4.1 14.1 - - + -
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Residues in contact with HIS 420 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418F HIS* 3.4 38.4 + + + +
419F ILE* 1.3 71.3 + - - +
421F LEU* 1.3 62.9 + - - +
422F MET* 3.9 10.3 + - + +
427F ALA* 3.4 5.0 - - - +
428F CYS* 2.9 53.4 + - + +
430F ALA* 6.0 4.7 - - + -
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Residues in contact with LEU 421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344F MET 5.9 2.9 - - - +
346F ARG* 4.3 33.4 - - + +
347F LYS* 4.3 25.4 - - + -
350F ILE* 4.6 1.1 - - + -
419F ILE* 3.9 25.0 + - + -
420F HIS* 1.3 73.0 - - - +
422F MET* 1.3 62.9 + - - +
423F GLY 3.8 9.8 + - - +
426F SER 4.4 1.6 - - - +
427F ALA* 4.0 14.8 - - + -
462F TRP* 6.4 0.4 - - + -
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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