Contacts of the helix formed by residues 613 - 623 (chain A) in PDB entry 1MS4
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 613 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610A ARG* 5.7 0.2 - - - +
611A GLN 3.6 1.9 + - - +
612A LEU* 1.3 76.2 - - - +
614A ALA* 1.3 60.4 + - - +
615A GLU* 3.2 9.2 + - - +
616A GLU* 2.8 48.8 + - - +
617A ILE* 2.9 30.1 + - - +
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Residues in contact with ALA 614 (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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559A TYR* 6.0 3.6 - - + -
613A ASN* 1.3 75.1 - - - +
615A GLU* 1.3 58.1 + - - +
617A ILE* 3.3 10.0 + - - +
618A ARG* 3.0 27.5 + - - +
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Residues in contact with GLU 615 (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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412A PRO* 3.7 27.6 - - + +
613A ASN* 3.2 9.9 + - - +
614A ALA* 1.3 77.2 - - - +
616A GLU* 1.3 64.7 + - + +
618A ARG* 3.2 6.5 + - + +
619A THR* 2.8 43.6 + - - +
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Residues in contact with GLU 616 (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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415A THR* 3.7 22.9 + - + +
610A ARG* 2.7 41.8 + - - -
612A LEU* 3.4 10.5 - - + -
613A ASN* 2.8 57.1 + - - +
615A GLU* 1.3 79.9 - - + +
617A ILE* 1.3 62.5 + - - +
619A THR* 3.4 6.2 + - - -
620A LEU* 3.1 29.6 + - - +
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Residues in contact with ILE 617 (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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546A HIS* 4.3 1.7 + - + -
548A VAL* 4.2 30.3 - - + -
550A THR* 4.6 3.6 - - + -
559A TYR* 3.8 47.8 - - + +
562A GLY* 4.2 23.3 - - - +
611A GLN* 6.0 0.2 - - + -
612A LEU* 3.9 27.8 - - + +
613A ASN 2.9 21.3 + - - +
614A ALA* 3.6 7.4 - - - +
615A GLU 3.2 0.2 - - - -
616A GLU* 1.3 76.1 - - - +
618A ARG* 1.3 62.0 + - - +
620A LEU* 3.1 10.5 + - - +
621A PHE* 3.0 19.9 + - - +
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Residues in contact with ARG 618 (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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562A GLY* 5.3 7.2 - - - +
563A GLU* 5.0 12.5 + - - -
614A ALA 3.0 17.2 + - - +
615A GLU* 3.2 7.8 + - + +
617A ILE* 1.3 77.3 - - - +
619A THR* 1.3 65.4 + - - +
621A PHE* 3.2 17.6 + - - +
622A LEU* 2.9 57.7 + - + +
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Residues in contact with THR 619 (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 THR* 3.8 17.6 - - + +
412A PRO* 3.0 49.6 - - + +
413A ALA 3.9 4.5 - - - +
414A VAL* 3.9 17.5 - - + +
615A GLU* 2.8 25.3 + - - +
616A GLU* 3.8 6.7 - - - -
618A ARG* 1.3 74.4 - - - +
620A LEU* 1.3 60.4 + - - +
622A LEU* 3.2 9.9 + - - +
623A SER* 2.7 26.5 + - - -
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Residues in contact with LEU 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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414A VAL* 4.1 24.0 - - + -
415A THR* 5.4 3.8 - - + +
485A VAL* 4.2 16.6 - - + -
546A HIS* 3.5 23.3 - - + +
548A VAL* 5.8 0.9 - - + -
606A LEU* 3.6 24.9 - - + -
608A TYR* 4.0 10.3 - - + +
612A LEU* 3.5 31.9 - - + -
616A GLU 3.1 15.5 + - - +
617A ILE* 3.6 7.6 - - - +
619A THR* 1.3 77.6 - - - +
621A PHE* 1.3 63.0 + - - +
623A SER* 3.2 19.4 + - - +
624A GLN* 3.3 8.0 + - - +
627A ILE* 4.7 10.4 - - + +
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Residues in contact with PHE 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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546A HIS* 3.3 32.2 + - + -
561A ASP* 3.2 57.7 - - + -
562A GLY* 4.3 8.7 - - - +
563A GLU* 6.1 0.2 - - - -
617A ILE 3.0 11.0 + - - +
618A ARG* 3.2 18.4 + - - +
620A LEU* 1.3 76.0 - - - +
622A LEU* 1.3 86.2 + - + +
623A SER 3.2 0.7 + - - -
624A GLN* 3.5 23.4 + - - +
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Residues in contact with LEU 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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397A THR* 5.9 0.2 - - - -
398A PRO* 3.4 50.8 - - + +
399A ALA 5.3 2.7 - - - +
618A ARG* 2.9 59.6 + - + +
619A THR* 3.7 7.4 - - - +
621A PHE* 1.3 96.2 - - + +
623A SER* 1.3 59.0 + - - +
624A GLN 3.5 0.7 + - - -
626A LEU* 4.6 1.9 - - - +
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Residues in contact with SER 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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395A ILE* 5.0 0.9 - - - -
397A THR* 4.5 10.5 - - - -
398A PRO* 4.7 0.9 - - - -
414A VAL* 3.8 21.4 - - - +
619A THR 2.7 17.8 + - - -
620A LEU* 3.2 11.7 + - - -
621A PHE 3.2 0.6 - - - -
622A LEU* 1.3 76.7 - - - +
624A GLN* 1.3 67.2 + - - +
625A ASP 3.2 2.7 - - - -
626A LEU* 2.8 33.7 + - - -
627A ILE* 3.4 16.5 + - - +
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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