Contacts of the helix formed by residues 645 - 653 (chain B) in PDB entry 5MKF
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 645 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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623B VAL* 4.9 7.6 - - + -
624B ASP* 4.6 7.0 - - - +
625B ASP* 2.9 39.2 + - + -
635B THR* 5.3 1.0 - - - +
638B ARG* 4.4 15.6 + - - +
639B ILE* 5.9 3.4 - - - +
643B ASP 4.3 0.6 + - - -
644B ILE* 1.3 75.0 - - - +
646B PHE* 1.3 48.6 - - - +
647B ALA* 2.6 20.4 + - - -
648B GLU* 2.5 49.3 + - - +
649B ILE* 3.3 11.5 + - + +
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Residues in contact with PHE 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625A ASP* 6.1 0.2 - - - -
631A GLU* 6.3 0.7 - - + -
634A PHE* 3.9 33.0 - + + -
635A THR* 5.7 1.8 - - - -
638A ARG* 4.1 31.6 - - + -
639B ILE* 6.3 0.4 - - + +
644B ILE* 3.0 28.8 - - + +
645B ASN* 1.3 75.3 - - - +
647B ALA* 1.3 57.8 + - - +
648B GLU 3.3 0.4 - - - -
649B ILE* 3.5 39.9 + - + +
650B GLU* 2.8 51.2 - - + +
657B GLY 4.8 2.0 - - - -
658B PRO* 5.1 3.4 - - + -
661B PHE* 3.6 40.4 - + + -
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Residues in contact with ALA 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A ARG* 5.1 10.9 - - - +
644B ILE* 3.9 8.5 - - + +
645B ASN* 2.6 8.8 + - - +
646B PHE* 1.3 77.0 - - - +
648B GLU* 1.3 64.7 + - + +
650B GLU* 3.1 13.8 + - - +
651B GLU* 4.5 4.0 + - - +
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Residues in contact with GLU 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623B VAL* 3.9 19.4 - - + +
624B ASP* 5.8 1.6 - - - -
645B ASN* 2.5 65.0 + - - +
647B ALA* 1.3 80.3 - - + +
649B ILE* 1.3 63.7 + - - -
650B GLU 3.3 0.9 - - - -
651B GLU* 3.4 23.6 + - + +
652B ALA* 3.1 19.8 + - - +
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Residues in contact with ILE 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619B PHE* 4.4 10.3 - - + -
623B VAL* 5.2 9.4 - - + -
626B PHE* 5.0 15.9 - - + -
639B ILE* 5.0 15.7 - - + -
645B ASN* 3.3 11.9 + - + +
646B PHE* 3.9 42.6 - - + +
647B ALA 3.4 1.4 - - - -
648B GLU* 1.3 73.4 - - - +
650B GLU* 1.3 69.0 + - - +
652B ALA* 2.9 22.4 + - - +
653B ASN 3.4 5.7 + - - +
657B GLY* 3.5 36.4 - - - +
658B PRO 4.5 0.2 - - - -
660B TYR* 5.6 6.7 - - + -
661B PHE* 5.2 7.0 - - + -
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Residues in contact with GLU 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631A GLU* 4.4 25.7 - - + +
634A PHE* 4.6 6.2 - - + -
646B PHE* 2.8 57.6 - - + +
647B ALA* 3.1 10.4 - - - +
649B ILE* 1.3 79.3 - - - +
651B GLU* 1.3 59.5 + - - +
652B ALA 2.8 7.3 + - - -
653B ASN 3.3 20.8 + - - -
654B ARG* 3.7 18.0 + - + +
658B PRO* 4.8 17.5 - - + -
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Residues in contact with GLU 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A SER* 6.0 1.6 - - - +
455A TRP* 2.2 64.7 + - + +
456A GLN* 5.3 3.1 + - - -
622B GLN* 5.8 1.9 - - - +
647B ALA 4.5 2.4 + - - +
648B GLU* 3.4 29.6 + - + +
649B ILE 3.2 0.8 - - - -
650B GLU* 1.3 78.4 - - - +
652B ALA* 1.3 67.5 + - - +
654B ARG* 5.4 13.8 + - - +
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Residues in contact with ALA 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A GLN* 4.4 13.0 + - - -
1006A PX6 5.7 0.3 + - - -
619B PHE* 4.1 21.5 - - + -
622B GLN* 3.4 34.8 + - + +
623B VAL* 5.1 8.7 - - + +
648B GLU 3.1 10.5 + - - +
649B ILE* 2.9 12.8 + - - +
650B GLU 2.8 1.8 + - - -
651B GLU* 1.3 86.2 - - - +
653B ASN* 1.3 62.0 + - + +
654B ARG* 5.9 0.9 + - - -
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Residues in contact with ASN 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A ILE* 4.6 16.1 - - - +
560A ASN* 4.8 4.4 - - - +
1006A PX6 3.4 18.4 + - - +
618B VAL* 5.0 3.8 - - + +
619B PHE* 5.0 6.7 - - + -
622B GLN* 5.4 1.8 - - - +
649B ILE 3.4 1.0 + - - -
650B GLU 3.3 4.1 + - - +
652B ALA* 1.3 82.9 - - + +
654B ARG* 1.3 63.2 + - - +
655B VAL* 3.3 17.5 + - - +
656B LEU* 3.3 37.9 - - + +
657B GLY* 2.9 31.0 + - - +
658B PRO* 3.5 3.1 - - - +
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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