Contacts of the helix formed by residues 617 - 626 (chain B) in PDB entry 4DBG
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 LEU 617 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL* 4.3 12.1 - - + -
69A VAL* 3.4 30.3 - - + -
71A ILE* 4.0 30.1 - - + -
92A TYR* 3.7 27.4 - - + -
94A PHE* 4.0 20.9 - - + -
613B GLN 3.0 14.8 + - - +
614B ARG* 3.5 6.7 + - - +
615B GLN 3.5 0.4 - - - -
616B ARG* 1.3 73.6 - - + +
618B GLU* 1.3 63.5 + - - +
619B PRO* 3.3 2.2 - - - -
620B PHE* 3.0 34.2 + - + +
621B ARG* 3.1 12.6 + - - +
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Residues in contact with GLU 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614B ARG* 3.4 14.1 + - - +
615B GLN* 3.3 17.9 - - - +
616B ARG 3.1 0.2 - - - -
617B LEU* 1.3 75.7 - - - +
619B PRO* 1.4 72.7 - - + +
621B ARG* 2.6 46.3 + - - +
622B GLN* 2.8 48.8 + - - +
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Residues in contact with PRO 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A MET* 6.1 0.2 - - + -
615B GLN 4.2 2.2 - - - +
616B ARG 3.4 16.8 - - - +
617B LEU 3.6 0.2 - - - -
618B GLU* 1.4 93.9 - - + +
620B PHE* 1.3 60.1 + - + +
622B GLN* 3.3 13.0 + - + +
623B ARG* 3.0 59.5 + - - +
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Residues in contact with PHE 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL* 3.6 33.7 - - + -
62A GLU* 3.8 10.5 - - - -
63A ASP* 3.3 31.6 - - + +
66A MET* 4.3 2.5 - - + -
67A HIS* 3.1 29.8 - - + -
68A THR 4.8 1.1 - - - -
69A VAL* 3.9 22.2 - - + -
94A PHE* 4.2 15.0 - - + -
130A LEU* 4.4 5.1 - - + +
616B ARG 4.8 2.9 - - - -
617B LEU* 3.0 26.3 + - + +
619B PRO* 1.3 79.0 - - + +
621B ARG* 1.3 69.1 + - - +
623B ARG* 3.3 30.2 + - - +
624B LEU* 3.4 16.5 + - - +
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Residues in contact with ARG 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A TYR 3.4 26.9 - - - +
93A GLY* 4.6 10.2 + - - +
94A PHE* 3.6 18.0 - - + -
614B ARG* 6.3 3.1 - - - +
617B LEU 3.1 6.9 + - - +
618B GLU* 2.6 52.1 + - - +
620B PHE* 1.3 77.9 - - - +
622B GLN* 1.3 71.6 + - - +
624B LEU* 3.1 23.9 + - + +
625B TRP* 3.3 33.8 + - - +
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Residues in contact with GLN 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618B GLU* 2.8 50.6 + - - +
619B PRO* 3.6 13.5 - - + +
621B ARG* 1.3 79.1 - - - +
623B ARG* 1.3 62.7 + - + +
625B TRP* 3.2 19.6 + - - +
626B ASP* 3.2 20.6 + - - +
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Residues in contact with ARG 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ASP* 3.0 25.5 + - - +
65A GLN* 3.7 38.2 + - - +
66A MET* 3.0 48.2 - - - +
132A SER* 3.9 12.4 - - - -
619B PRO* 3.0 51.9 + - - +
620B PHE* 3.3 21.4 + - - +
622B GLN* 1.3 69.8 - - - +
624B LEU* 1.3 65.0 + - + +
625B TRP 3.0 3.4 + - - -
626B ASP* 3.4 26.3 + - + +
627B SER 4.6 2.1 + - - -
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Residues in contact with LEU 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ASP* 5.9 2.5 - - + +
93A GLY 4.3 3.1 - - - +
94A PHE* 3.4 44.2 - - + -
95A PRO* 4.3 6.3 - - + -
98A LEU* 4.1 17.9 - - + -
130A LEU* 4.2 17.7 - - + -
131A LEU 3.2 25.8 - - - +
132A SER* 4.3 3.4 - - - -
133A ALA* 2.9 32.2 + - - +
620B PHE 3.4 8.6 + - - +
621B ARG* 3.1 18.7 + - + +
623B ARG* 1.3 80.2 - - + +
625B TRP* 1.3 78.1 + - + +
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Residues in contact with TRP 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE* 6.3 0.4 - + - -
93A GLY 4.4 7.0 - - - -
95A PRO* 4.0 34.3 - - + -
98A LEU* 4.9 8.3 - - + -
133A ALA* 4.7 14.9 - - + +
621B ARG* 3.3 47.3 + - - +
622B GLN* 3.2 7.5 + - - +
623B ARG 3.0 0.2 - - - -
624B LEU* 1.3 93.7 - - + +
626B ASP* 1.3 64.9 + - - +
627B SER 4.0 0.6 - - - -
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Residues in contact with ASP 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLN* 5.8 2.2 - - - +
133A ALA* 5.9 0.2 - - - -
622B GLN* 3.2 26.6 + - - +
623B ARG* 3.4 25.5 + - + +
625B TRP* 1.3 79.7 - - - +
627B SER* 1.3 72.2 + - - +
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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