Contacts of the helix formed by residues 625 - 637 (chain d) 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 d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619d GLU* 5.3 8.5 - - + +
620d MET* 4.4 4.9 - - - +
623d GLY* 3.3 4.3 - - - +
624d ASP* 1.3 75.9 - - + +
626d VAL* 1.3 63.2 + - - +
627d GLU* 3.6 10.9 + - + +
628d ASN* 3.3 34.1 + - - +
629d ARG* 3.9 18.1 + - - +
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Residues in contact with VAL 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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178c GLY 3.3 26.5 - - - +
624d ASP 3.4 10.3 + - - +
625d VAL* 1.3 71.6 - - - +
627d GLU* 1.3 60.6 + - - +
629d ARG* 3.3 32.5 + - - +
630d ARG* 2.9 25.9 + - + +
17e G 4.1 13.5 - - + +
18e C 3.4 27.4 - - - +
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Residues in contact with GLU 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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625d VAL* 3.4 7.9 - - + +
626d VAL* 1.3 79.0 - - - +
628d ASN* 1.3 62.8 + - - +
630d ARG* 3.1 43.3 + - - +
631d GLN* 2.9 37.2 + - + +
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Residues in contact with ASN 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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619d GLU* 5.9 0.8 + - - -
620d MET* 3.9 26.2 - - + +
625d VAL* 3.3 32.5 - - - +
626d VAL 3.4 0.4 - - - -
627d GLU* 1.3 80.1 - - - +
629d ARG* 1.3 58.1 + - - +
631d GLN* 3.5 7.3 + - - +
632d PHE* 3.0 28.9 + - - +
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Residues in contact with ARG 629 (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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22c PHE* 3.6 26.0 - - + -
177c VAL* 4.1 5.3 - - + +
178c GLY* 4.0 4.2 - - - +
466d LYS* 3.4 9.7 - - - +
620d MET* 3.5 17.9 + - - +
621d LEU* 2.9 30.7 - - + +
623d GLY 3.1 24.2 + - - -
624d ASP 4.6 3.0 + - - -
625d VAL 3.9 3.7 + - - +
626d VAL* 3.3 38.7 + - - +
628d ASN* 1.3 75.2 - - - +
630d ARG* 1.3 64.0 + - - +
632d PHE* 3.4 6.9 + - - +
633d ILE* 3.2 29.4 + - + +
16e C 4.1 0.4 - - - -
17e G 1.7 58.2 + - - -
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Residues in contact with ARG 630 (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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178c GLY* 3.2 34.9 - - - +
179c MET* 4.5 6.3 - - + -
626d VAL* 2.9 9.8 + - + +
627d GLU* 3.1 44.7 + - - +
629d ARG* 1.3 72.5 - - - +
631d GLN* 1.3 81.9 + - - +
633d ILE* 3.2 9.2 + - - +
634d GLU* 3.0 50.0 + - - +
701d JK8 3.4 50.9 + - - +
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Residues in contact with GLN 631 (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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627d GLU* 2.9 25.1 + - + +
628d ASN* 3.5 9.4 - - - +
629d ARG 3.3 0.2 - - - -
630d ARG* 1.3 101.6 + - - +
632d PHE* 1.3 57.1 + - - +
634d GLU* 3.3 12.4 + - - +
635d ASP* 2.9 68.3 + - - +
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Residues in contact with PHE 632 (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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19c ARG* 3.3 57.0 - - + -
22c PHE* 4.6 2.7 - + - -
23c LEU* 4.1 23.8 - - + -
620d MET* 3.7 26.5 - - + -
621d LEU* 3.3 26.2 - - + -
628d ASN 3.0 14.7 + - - +
629d ARG 3.4 11.7 - - - +
631d GLN* 1.3 76.0 - - - +
633d ILE* 1.3 63.2 + - + +
635d ASP* 4.5 4.5 - - - -
636d ASN* 2.9 64.6 + - - +
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Residues in contact with ILE 633 (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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22c PHE* 4.7 4.0 - - + -
23c LEU* 3.9 8.5 - - + -
26c ALA* 3.4 30.5 - - + -
27c MET* 3.4 23.4 - - + +
30c ILE* 3.8 19.5 - - + -
177c VAL* 3.9 30.1 - - + +
178c GLY 4.5 0.4 - - - +
629d ARG 3.2 20.1 + - - +
630d ARG* 3.2 9.2 + - - +
632d PHE* 1.3 83.1 - - + +
634d GLU* 1.3 55.0 + - - +
636d ASN 3.3 1.6 + - - -
637d ALA* 2.8 34.8 + - - +
701d JK8 3.8 9.6 - - + +
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Residues in contact with GLU 634 (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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630d ARG* 3.0 33.3 + - - +
631d GLN* 3.7 16.9 + - - +
633d ILE* 1.3 77.2 - - - +
635d ASP* 1.3 64.8 + - - +
636d ASN 3.4 0.2 + - - -
637d ALA* 3.4 12.6 + - - +
701d JK8 3.2 76.2 + - + +
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Residues in contact with ASP 635 (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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631d GLN* 2.9 54.2 + - - +
632d PHE* 3.6 3.4 + - - +
634d GLU* 1.3 79.7 - - - +
636d ASN* 1.3 72.5 + - - +
637d ALA 3.8 2.4 + - - +
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Residues in contact with ASN 636 (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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19c ARG* 3.6 20.9 + - - +
23c LEU* 3.3 36.9 - - + +
632d PHE* 2.9 47.8 + - + +
633d ILE 3.5 1.1 - - - -
635d ASP* 1.3 85.5 - - - +
637d ALA* 1.3 65.8 + - - +
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Residues in contact with ALA 637 (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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23c LEU* 5.2 0.2 - - - -
27c MET* 3.4 25.4 - - + -
633d ILE 2.8 16.4 + - - +
634d GLU 3.4 7.7 + - - +
635d ASP 3.5 2.8 - - - +
636d ASN* 1.3 82.3 - - - +
701d JK8 3.5 49.2 - - + -
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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