Contacts of the helix formed by residues 625 - 637 (chain M) in PDB entry 6QX2
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 VAL 625 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619M GLU 5.4 3.4 - - - +
620M MET 4.4 2.8 - - - +
623M GLY* 3.3 2.5 - - - +
624M ASP* 1.3 76.5 - - + +
626M VAL* 1.3 63.0 + - - +
627M GLU* 3.6 11.2 + - + +
628M ASN* 3.3 35.9 + - - +
629M ARG* 3.8 20.4 + - - -
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Residues in contact with VAL 626 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178L GLY* 3.2 36.3 - - - +
624M ASP 3.4 8.9 + - - +
625M VAL* 1.3 71.6 - - - +
627M GLU* 1.3 61.3 + - - +
629M ARG* 3.3 24.1 + - - +
630M ARG* 2.9 25.2 + - + +
2017N G 3.9 24.5 - - + +
2018N C 3.6 28.0 - - - +
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Residues in contact with GLU 627 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625M VAL* 3.4 9.2 - - + +
626M VAL* 1.3 79.5 - - - +
628M ASN* 1.3 61.6 + - - +
630M ARG* 3.1 42.2 + - - +
631M GLN* 2.9 35.7 + - + +
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Residues in contact with ASN 628 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620M MET* 3.9 26.0 - - + +
625M VAL* 3.3 33.0 + - - +
626M VAL 3.4 0.4 - - - -
627M GLU* 1.3 79.6 - - - +
629M ARG* 1.3 58.1 + - - +
631M GLN* 3.5 7.1 + - - +
632M PHE* 3.0 28.4 + - - +
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Residues in contact with ARG 629 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L PHE* 3.4 39.7 - - + -
177L VAL* 3.8 6.1 - - + -
178L GLY* 4.7 1.3 - - - -
466M LYS* 3.8 7.7 - - - +
620M MET* 3.5 23.4 + - - +
621M LEU* 2.8 32.0 + - + +
622M MET* 4.0 1.2 - - - +
623M GLY 2.8 30.7 + - - +
624M ASP 4.1 2.2 - - - -
625M VAL 3.8 5.6 + - - +
626M VAL* 3.3 25.2 + - - +
628M ASN* 1.3 75.5 - - - +
630M ARG* 1.3 63.3 + - - +
632M PHE* 3.4 9.3 + - - +
633M ILE* 3.2 33.6 + - + +
2016N C 4.4 1.2 + - - -
2017N G 2.8 42.7 + - - +
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Residues in contact with ARG 630 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178L GLY* 3.5 33.2 - - - +
179L MET* 3.8 23.3 - - + -
501L JK8 2.8 55.4 + - + +
626M VAL 2.9 13.4 + - - +
627M GLU* 3.1 31.4 + - - +
629M ARG* 1.3 72.0 - - - +
631M GLN* 1.3 96.7 + - - +
633M ILE* 3.2 8.7 + - - +
634M GLU* 3.0 39.2 + - - +
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Residues in contact with GLN 631 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627M GLU* 2.9 24.2 + - + +
628M ASN* 3.5 9.2 - - - +
629M ARG 3.3 0.2 - - - -
630M ARG* 1.3 102.4 + - - +
632M PHE* 1.3 55.4 + - - +
634M GLU* 3.3 12.1 + - - +
635M ASP* 2.9 67.1 + - - +
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Residues in contact with PHE 632 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L ARG* 3.3 54.7 - - + -
22L PHE* 4.7 2.9 - + - -
23L LEU* 4.0 27.1 - - + -
620M MET* 3.7 26.2 - - + -
621M LEU* 3.3 26.2 - - + -
628M ASN 3.0 14.5 + - - +
629M ARG* 3.4 12.3 - - - +
631M GLN* 1.3 75.7 - - - +
633M ILE* 1.3 62.9 + - + +
635M ASP* 3.5 4.4 + - - -
636M ASN* 2.9 63.6 + - + +
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Residues in contact with ILE 633 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L PHE* 5.2 0.4 - - + -
23L LEU* 4.0 8.9 - - + +
26L ALA* 3.6 28.7 - - + -
27L MET* 3.8 28.3 - - + -
30L ILE* 3.9 16.6 - - + -
177L VAL* 3.9 28.3 - - + +
179L MET* 6.2 0.4 - - + -
501L JK8 4.0 8.5 - - + -
629M ARG* 3.2 24.5 + - + +
630M ARG* 3.2 9.8 + - + +
632M PHE* 1.3 82.2 - - + +
634M GLU* 1.3 56.4 + - - +
636M ASN 3.3 1.7 + - - -
637M ALA* 2.8 37.4 + - - +
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Residues in contact with GLU 634 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501L JK8 3.4 67.1 + - + +
630M ARG* 3.0 34.6 + - - +
631M GLN* 3.7 14.7 + - - +
633M ILE* 1.3 77.3 - - - +
635M ASP* 1.3 66.5 + - - +
637M ALA* 3.4 11.3 + - - +
638M VAL* 5.0 1.6 + - - +
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Residues in contact with ASP 635 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631M GLN* 2.9 53.3 + - - +
632M PHE* 3.6 2.3 + - - +
634M GLU* 1.3 79.9 - - - +
636M ASN* 1.3 71.5 + - - +
637M ALA 3.8 0.3 + - - -
638M VAL* 4.8 3.3 + - - +
639M TYR* 4.9 4.7 - - - +
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Residues in contact with ASN 636 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L ARG* 3.5 20.7 + - - +
23L LEU* 3.4 35.8 - - + +
632M PHE* 2.9 48.6 + - + +
633M ILE 3.5 1.3 - - - -
635M ASP* 1.3 85.6 - - - +
637M ALA* 1.3 63.5 - - - +
638M VAL 3.3 3.6 + - - -
639M TYR* 3.4 34.0 + - + +
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Residues in contact with ALA 637 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L LEU* 5.7 0.2 - - - +
27L MET* 3.7 26.2 - - - +
501L JK8 3.6 48.1 - - + -
633M ILE 2.8 16.0 + - - +
634M GLU 3.4 7.3 + - - +
635M ASP 3.5 0.2 - - - -
636M ASN* 1.3 78.9 - - - +
638M VAL* 1.3 58.1 + - - +
639M TYR 4.5 2.1 - - - +
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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