Contacts of the helix formed by residues 622 - 634 (chain T) in PDB entry 6FF7
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 ARG 622 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571T SER 5.4 0.2 - - - -
620T ASN* 2.5 18.4 + - + +
621T PRO* 1.3 74.7 - - - +
623T ASN* 1.3 52.9 + - - +
624T THR 3.0 2.9 - - - +
625T ARG* 3.0 5.6 + - - +
626T PHE* 2.7 37.0 + - - +
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Residues in contact with ASN 623 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570T LEU* 4.2 17.7 - - - +
571T SER* 4.0 16.4 - - - +
617T PRO* 4.4 15.5 - - + +
619T ASP* 5.9 5.2 - - + -
620T ASN* 3.7 3.5 + - - +
622T ARG* 1.3 79.6 - - + +
624T THR* 1.3 57.2 + - - +
626T PHE* 3.7 10.2 - - - +
627T ALA* 3.2 24.1 + - - +
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Residues in contact with THR 624 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617T PRO 3.6 21.2 + - - -
618T ARG* 4.8 3.8 - - - -
619T ASP* 4.0 9.1 + - - +
620T ASN 3.5 17.3 + - - -
621T PRO* 4.5 5.6 - - - -
622T ARG 3.0 0.4 - - - -
623T ASN* 1.3 77.4 - - - +
625T ARG* 1.3 65.9 + - - +
626T PHE 3.2 0.3 + - - -
627T ALA* 3.3 12.3 + - - +
628T ILE* 3.4 12.8 + - - +
643T LEU* 5.5 10.1 - - - -
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Residues in contact with ARG 625 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621T PRO* 4.1 15.2 - - + +
622T ARG* 3.0 10.1 + - - +
624T THR* 1.3 79.1 - - - +
626T PHE* 1.3 56.7 + - - +
628T ILE* 3.4 7.5 + - - +
629T ASN* 2.9 29.2 + - - +
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Residues in contact with PHE 626 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5483 PHE* 6.5 1.8 - - + -
571T SER 3.7 23.3 - - - +
572T GLU* 3.7 17.3 - - + +
622T ARG 2.7 21.2 + - - +
623T ASN* 3.9 4.3 - - - +
624T THR 3.1 0.4 - - - -
625T ARG* 1.3 71.2 - - - +
627T ALA* 1.3 65.7 + - - +
629T ASN* 3.8 5.8 - - - +
630T PHE* 2.8 26.0 + - - +
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Residues in contact with ALA 627 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570T LEU* 5.5 7.8 - - + +
614T GLY 4.6 14.8 - - - +
615T LEU* 4.7 13.5 - - - +
617T PRO* 5.5 2.7 - - + +
623T ASN 3.2 15.5 + - - +
624T THR* 3.3 9.8 + - - +
626T PHE* 1.3 74.8 - - - +
628T ILE* 1.3 65.0 + - - +
630T PHE* 2.9 16.9 + - - +
631T PHE* 2.9 16.8 + - - +
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Residues in contact with ILE 628 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624T THR 3.4 9.6 + - - +
625T ARG* 3.7 8.5 - - - +
627T ALA* 1.3 78.0 - - - +
629T ASN* 1.3 64.4 + - - +
631T PHE* 3.4 3.5 + - - +
632T THR* 2.9 26.1 + - - -
639T LEU 5.4 2.9 - - - -
640T THR* 4.9 20.4 - - - -
641T ASP 5.6 4.9 - - - +
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Residues in contact with ASN 629 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5483 PHE* 5.2 14.8 - - + -
625T ARG 2.9 17.6 + - - +
626T PHE* 3.8 6.7 - - - +
628T ILE* 1.3 76.5 - - - +
630T PHE* 1.3 64.2 + - - +
632T THR* 3.2 5.9 + - - -
633T SER* 2.9 23.5 + - - -
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Residues in contact with PHE 630 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5443 PRO* 4.4 8.0 - - + +
5453 MET* 6.0 6.5 - - + +
626T PHE 2.8 19.2 + - - +
627T ALA* 2.9 6.8 + - - +
629T ASN* 1.3 75.2 - - - +
631T PHE* 1.3 57.8 + - - +
633T SER* 2.7 24.8 + - - -
634T ILE* 2.8 16.2 + - - +
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Residues in contact with PHE 631 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627T ALA 2.9 16.8 + - - +
628T ILE* 4.3 2.7 - - - +
630T PHE* 1.3 73.4 - - - +
632T THR* 1.3 58.7 + - - +
633T SER 3.3 0.2 - - - -
634T ILE* 4.1 7.7 - - - -
635T GLY 3.5 1.4 + - - -
636T LEU* 3.0 18.6 + - + +
637T GLY* 2.9 28.4 + - - +
638T GLY 5.7 0.4 - - - +
639T LEU 4.7 13.9 - - - +
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Residues in contact with THR 632 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628T ILE 2.9 18.2 + - - -
629T ASN* 3.6 6.5 - - - -
631T PHE* 1.3 79.2 - - - +
633T SER* 1.3 61.2 + - - +
635T GLY* 3.3 12.3 + - - -
636T LEU 4.8 0.2 - - - +
637T GLY* 4.4 11.4 - - - +
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Residues in contact with SER 633 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5443 PRO* 3.1 37.3 - - - +
629T ASN 2.9 11.6 + - - -
630T PHE* 2.7 12.9 + - - -
632T THR* 1.3 69.5 - - - +
634T ILE* 1.3 59.0 + - - -
635T GLY* 2.8 11.8 + - - -
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Residues in contact with ILE 634 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5443 PRO* 3.8 9.7 - - + +
584T LYS* 5.0 21.1 - - + +
587T PHE* 6.4 2.2 - - + -
588T GLN* 4.6 17.3 - - + +
630T PHE 2.8 13.9 + - - +
631T PHE* 4.3 9.0 - - - +
633T SER* 1.3 75.9 - - - +
635T GLY* 1.3 61.3 + - - +
636T LEU* 4.8 4.7 - - + +
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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