Contacts of the helix formed by residues 621 - 628 (chain D) in PDB entry 2C10
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 MET 621 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215D PRO* 3.8 27.4 - - + -
217D GLY 5.4 1.3 - - - +
381D THR* 5.5 3.4 - - + +
383D ARG* 3.6 36.8 - - - -
615D LEU* 3.8 8.5 - - + -
619D SER* 3.1 14.0 + - - +
620D SER* 1.3 78.5 + - - +
622D ALA* 1.3 59.4 + - - +
623D ARG 3.2 2.9 - - - -
624D GLY* 2.8 25.2 + - - -
625D PHE* 3.8 11.3 - - + -
653D PRO* 3.7 25.1 - - + +
654D TRP* 3.9 23.1 - - + +
1779D CL 4.2 13.9 - - + -
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Residues in contact with ALA 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615D LEU* 4.3 9.9 - - + +
616D PRO 3.7 18.8 - - - +
617D GLN* 4.1 13.9 - - + +
619D SER* 3.2 22.0 + - - +
620D SER 3.5 0.4 - - - -
621D MET* 1.3 77.7 - - - +
623D ARG* 1.3 60.2 + - + +
624D GLY 3.0 5.4 + - - -
625D PHE* 3.0 30.0 + - - -
626D SER* 3.3 12.9 + - - -
629D ARG* 5.8 4.3 - - - -
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Residues in contact with ARG 623 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617D GLN* 5.9 6.5 - - - +
619D SER 5.6 1.6 - - - +
620D SER 5.4 5.8 - - - +
621D MET 3.2 1.3 - - - -
622D ALA* 1.3 77.1 - - + +
624D GLY* 1.3 57.6 + - - +
625D PHE 3.1 2.7 + - - -
626D SER* 4.0 13.3 + - - -
653D PRO 5.0 1.1 - - - +
656D PRO* 3.6 25.4 - - + +
658D VAL 4.1 0.5 - - - +
659D ASP* 3.2 45.0 + - - +
661D SER* 3.8 23.2 + - - -
662D ASP* 5.0 7.5 + - - -
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Residues in contact with GLY 624 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D VAL* 4.7 4.3 - - - +
621D MET 2.8 14.7 + - - -
623D ARG* 1.3 77.8 - - - +
625D PHE* 1.3 69.9 + - - +
627D TRP* 5.1 0.3 + - - -
645D SER* 5.1 1.2 + - - -
649D ASN* 2.9 33.4 + - - +
653D PRO* 3.7 24.9 + - - +
656D PRO* 4.1 2.5 - - - -
658D VAL 5.1 0.4 - - - -
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Residues in contact with PHE 625 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369D LEU* 3.6 31.4 - - + -
371D ILE* 4.1 7.6 - - + -
383D ARG* 4.4 13.2 - - + -
385D VAL* 3.7 26.2 - - + -
615D LEU* 3.8 33.7 - - + -
621D MET* 3.8 26.9 - - + -
622D ALA* 3.0 12.2 + - - -
624D GLY* 1.3 86.0 - - - +
626D SER* 1.3 58.6 + - - +
627D TRP* 3.0 35.6 + - + +
628D GLU* 3.1 28.2 + - - +
649D ASN* 5.2 0.2 - - - +
653D PRO* 4.7 6.1 - - + -
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Residues in contact with SER 626 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622D ALA 3.3 10.3 + - - -
623D ARG* 4.0 10.1 + - - -
625D PHE* 1.3 70.6 - - - +
627D TRP* 1.3 57.5 + - - +
628D GLU 2.9 10.1 + - - -
629D ARG* 3.1 33.0 + - - +
630D TYR* 3.6 9.5 - - - -
659D ASP* 2.9 24.0 + - - -
660D PHE* 3.2 16.2 + - - +
661D SER* 3.3 22.0 + - - -
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Residues in contact with TRP 627 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D GLU* 3.8 34.7 - - + +
369D LEU* 3.6 37.2 - - + -
523D SER* 3.6 23.3 - - - -
524D ALA* 3.7 14.6 - - - -
525D HIS* 3.4 42.5 + + + +
625D PHE* 3.7 26.1 - - + +
626D SER* 1.3 79.4 + - - +
628D GLU* 1.3 61.9 + - - +
629D ARG 3.2 0.8 + - - -
630D TYR* 3.5 9.0 + - - +
644D SER* 4.1 20.6 - - - -
645D SER* 4.7 2.4 + - - -
660D PHE* 3.6 21.6 - - + +
679D THR* 2.9 45.6 + - + -
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Residues in contact with GLU 628 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369D LEU* 3.5 26.5 - - + +
371D ILE* 3.4 21.3 - - - +
521D THR* 4.2 8.3 + - - -
523D SER* 3.8 20.5 + - - +
579D VAL* 3.3 17.0 - - - +
612D GLY 5.1 3.7 - - - +
613D GLU 4.5 1.7 - - - +
614D PRO* 3.5 26.8 - - + +
615D LEU* 3.2 19.8 + - - +
625D PHE* 3.1 20.7 + - - +
626D SER 2.9 0.4 - - - -
627D TRP* 1.3 85.6 - - + +
629D ARG* 1.3 62.7 + - + +
630D TYR 3.2 2.6 - - - +
679D THR* 4.5 5.0 - - + +
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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