Contacts of the helix formed by residues 630 - 638 (chain A) in PDB entry 3UGM
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 PRO 630 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A GLY 5.5 5.8 - - - +
594A LEU* 4.5 17.3 - - + -
598A GLN* 5.8 0.4 - - - +
619A LEU* 4.9 8.9 - - + +
623A CYS* 4.6 11.7 - - - -
629A THR* 1.4 89.5 - - - +
631A ASP* 1.3 77.0 + - - +
633A VAL* 2.9 14.2 + - - +
634A VAL* 2.9 20.4 + - + +
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Residues in contact with ASP 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A GLN* 5.1 4.5 - - - +
629A THR* 3.2 5.8 + - - +
630A PRO* 1.3 85.1 - - - +
632A GLN* 1.3 54.5 + - - +
633A VAL 2.6 13.0 + - - -
634A VAL* 3.4 13.6 - - + +
635A ALA* 3.0 26.9 + - - +
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Residues in contact with GLN 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627A GLY 3.8 4.4 + - - +
628A LEU* 2.9 41.1 - - + +
629A THR* 2.7 37.3 + - + +
631A ASP* 1.3 70.7 - - - +
633A VAL* 1.3 56.9 + - - +
635A ALA* 4.5 3.1 - - - -
636A ILE* 3.4 8.4 - - - +
664A PRO* 4.2 15.2 + - - +
665A ASP* 4.4 3.2 - - - +
668A VAL* 2.8 63.7 - - + +
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Residues in contact with VAL 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A VAL* 5.3 5.8 - - + -
619A LEU* 4.1 24.9 - - + +
622A LEU* 4.2 21.8 - - + -
623A CYS* 6.3 0.2 - - - -
628A LEU* 3.8 37.2 - - + -
629A THR 3.9 7.2 + - - +
630A PRO 2.9 6.1 + - - +
631A ASP 2.6 6.5 + - - -
632A GLN* 1.3 73.8 - - - +
634A VAL* 1.3 57.9 + - - +
635A ALA 2.9 1.6 - - - -
636A ILE* 2.6 39.8 + - + +
637A ALA* 3.0 4.9 + - - +
646A LEU* 3.7 21.3 - - + +
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Residues in contact with VAL 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A LEU* 3.8 21.1 - - + -
598A GLN* 3.0 46.9 - - - +
602A ILE* 4.7 2.7 - - + -
615A VAL* 5.6 2.7 - - + -
619A LEU* 5.5 1.8 - - + -
630A PRO* 2.9 22.0 + - + +
631A ASP* 3.4 15.9 - - + +
633A VAL* 1.3 74.9 - - + +
635A ALA* 1.3 58.2 + - + +
636A ILE 2.8 2.9 + - - -
637A ALA* 2.9 9.2 + - - +
638A SER* 2.5 40.6 + - - +
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Residues in contact with ALA 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631A ASP 3.0 14.3 + - - +
632A GLN* 4.5 7.2 - - - +
633A VAL 2.9 0.6 - - - -
634A VAL* 1.3 79.6 - - + +
636A ILE* 1.3 55.4 + - - +
638A SER* 3.6 13.5 - - - +
639A ASN* 4.6 7.0 - - - +
668A VAL* 5.3 2.9 - - + -
672A SER* 2.6 32.7 + - - +
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Residues in contact with ILE 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622A LEU* 6.4 0.2 - - + -
628A LEU* 4.4 8.7 - - + -
632A GLN 3.4 23.6 - - - +
633A VAL* 2.6 32.0 + - + +
635A ALA* 1.3 77.6 - - - +
637A ALA* 1.3 67.4 + - - +
639A ASN* 3.9 6.5 + - - +
641A GLY* 4.6 0.3 - - - -
642A GLY 3.5 17.6 + - - -
645A ALA* 4.3 2.2 - - + -
646A LEU* 4.2 30.3 - - + +
649A VAL* 4.7 8.5 - - + -
668A VAL* 4.0 10.8 - - + -
671A ALA* 3.1 45.2 - - + +
672A SER* 4.0 8.1 - - - +
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Residues in contact with ALA 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A ILE* 2.7 33.2 - - + +
605A ASN* 3.7 5.0 + - - -
611A ALA* 4.8 6.4 - - + +
615A VAL* 4.1 17.0 - - + -
633A VAL 3.0 5.3 + - - +
634A VAL* 3.2 15.5 - - - +
636A ILE* 1.3 76.6 - - - +
638A SER* 1.4 53.4 + - - +
639A ASN 2.6 27.5 - - - +
642A GLY* 4.3 15.1 + - - -
646A LEU* 4.9 4.5 - - + +
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Residues in contact with SER 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A GLN* 5.1 0.9 - - - -
601A ALA* 3.3 39.7 - - - +
602A ILE* 3.6 5.6 - - - +
605A ASN* 3.0 23.0 + - - +
634A VAL* 2.5 37.5 + - - +
635A ALA* 3.6 12.3 - - - +
637A ALA* 1.4 67.2 - - - +
639A ASN* 1.3 56.3 + - - +
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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