Contacts of the helix formed by residues 619 - 628 (chain A) in PDB entry 5I4E
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 ASN 619 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414A ALA 2.8 27.7 + - - -
415A LEU* 4.1 4.2 + - - +
418A PRO* 3.4 22.5 - - - +
431A GLN* 5.4 2.3 - - - +
439A ALA* 4.7 15.9 - - + +
443A LEU* 4.6 15.1 - - + +
618A LEU* 1.3 75.2 - - - +
620A ASP* 1.3 67.2 + - - +
621A ASN* 3.7 4.9 + - - +
622A VAL* 3.1 33.6 - - + +
623A ALA* 3.2 24.3 + - - +
646A GLY* 5.7 1.0 + - - +
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Residues in contact with ASP 620 (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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419A ARG 5.5 2.4 - - - +
618A LEU 3.3 5.2 + - - -
619A ASN* 1.3 75.7 + - - +
621A ASN* 1.3 66.7 + - - +
623A ALA* 3.8 4.6 - - - +
624A ALA* 3.1 27.5 + - - +
641A VAL* 5.2 7.4 - - - +
645A VAL* 3.0 52.6 - - + +
646A GLY 4.6 2.4 - - - +
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Residues in contact with ASN 621 (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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414A ALA* 3.5 23.8 - - + +
418A PRO* 2.8 17.6 - - - +
419A ARG* 2.6 62.0 + - - +
420A ILE* 5.2 1.0 - - - +
619A ASN* 3.3 7.6 + - - +
620A ASP* 1.3 81.1 - - - +
622A VAL* 1.3 58.3 + - - +
624A ALA* 3.8 5.4 + - - +
625A LEU* 3.1 28.4 + - - +
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Residues in contact with VAL 622 (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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375A PHE* 5.5 1.6 - - + -
406A LEU* 5.3 0.4 - - + -
411A PHE* 3.9 27.8 - - + -
414A ALA* 3.8 14.1 - - + -
415A LEU* 3.9 13.0 - - - +
443A LEU* 3.6 39.5 - - + -
619A ASN* 3.1 24.3 + - + +
620A ASP 3.4 0.4 - - - -
621A ASN* 1.3 74.1 - - - +
623A ALA* 1.4 60.8 + - - +
625A LEU* 3.0 11.3 + - + +
626A LEU* 2.9 38.7 + - + +
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Residues in contact with ALA 623 (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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443A LEU* 4.5 3.0 - - + +
618A LEU* 5.2 7.6 - - + -
619A ASN 3.2 20.4 + - - +
620A ASP* 3.8 6.3 - - - +
622A VAL* 1.4 72.4 - - - +
624A ALA* 1.4 57.0 + - - +
626A LEU* 3.1 9.9 + - - +
627A HIS* 3.0 27.0 + - - +
638A TRP* 4.1 29.5 - - + -
641A VAL* 4.5 19.5 - - + +
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Residues in contact with ALA 624 (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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620A ASP* 3.1 21.9 + - - +
621A ASN* 3.8 7.2 - - - +
623A ALA* 1.4 74.1 - - - +
625A LEU* 1.3 63.8 + - + +
627A HIS* 3.2 11.7 + - - +
628A GLN* 3.1 37.2 + - - +
641A VAL* 5.2 5.3 - - + +
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Residues in contact with LEU 625 (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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406A LEU* 3.3 22.9 - - + +
407A GLY 5.5 0.2 - - - +
410A ASP* 3.4 55.4 - - + +
411A PHE* 3.7 10.8 - - + +
414A ALA* 3.5 16.4 - - + -
621A ASN 3.1 16.4 + - - +
622A VAL* 3.0 11.1 + - + +
624A ALA* 1.3 78.4 - - + +
626A LEU* 1.3 62.3 + - - +
628A GLN* 3.1 27.6 + - - +
629A SER 3.2 9.2 + - - -
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Residues in contact with LEU 626 (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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375A PHE* 5.0 5.2 - - + -
404A LEU* 3.9 18.8 - - + -
406A LEU* 3.5 32.3 - - + -
443A LEU* 4.1 17.9 - - + -
447A THR* 4.5 4.0 - - - +
622A VAL* 2.9 24.3 + - + +
623A ALA 3.1 6.9 + - - +
625A LEU* 1.3 74.0 - - - +
627A HIS* 1.3 58.7 + - - +
629A SER* 3.1 20.7 - - - -
634A THR* 3.7 16.0 - - + +
635A ALA* 3.8 2.8 - - - -
638A TRP* 3.4 56.2 - - + +
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Residues in contact with HIS 627 (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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623A ALA 3.0 11.3 + - - +
624A ALA* 3.2 15.5 - - - +
626A LEU* 1.3 76.2 - - - +
628A GLN* 1.4 65.9 + - + +
629A SER 3.2 2.5 + - - -
635A ALA* 4.0 14.7 - - - +
638A TRP* 2.9 29.5 + - - +
639A LYS* 3.0 31.2 + - + -
641A VAL* 4.1 12.4 - - + +
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Residues in contact with GLN 628 (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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405A GLY 5.0 0.2 - - - +
624A ALA* 3.1 28.5 + - - +
625A LEU* 3.1 21.6 + - - +
627A HIS* 1.4 83.4 - - + +
629A SER* 1.3 62.6 + - - +
630A THR* 3.7 3.5 + - - +
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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