Contacts of the helix formed by residues 399 - 404 (chain C) in PDB entry 1D7W
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 399 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A PHE* 4.0 12.8 - - + -
73A THR* 5.3 7.6 - - + +
76A LEU* 3.8 20.6 - - + -
336C HIS 5.6 0.2 + - - -
339C ILE* 3.9 14.4 - - + +
340C GLN 4.6 1.3 - - - +
341C PRO* 4.3 16.8 - - + -
390C LYS* 3.7 28.5 - - + +
398C ALA* 1.3 73.1 - - - +
400C ASP* 1.3 59.6 + - - +
401C GLU* 3.8 20.4 - - + +
402C ILE* 3.1 24.7 + - + +
403C ARG* 2.9 23.6 + - - +
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Residues in contact with ASP 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ARG* 4.4 16.6 + - - +
71A PHE 4.7 11.2 + - - +
73A THR* 4.6 3.2 + - - +
1602A SO4 3.4 24.3 + - - +
398C ALA 4.0 0.2 + - - -
399C VAL* 1.3 70.3 - - - +
401C GLU* 1.3 61.5 + - - +
402C ILE 3.1 2.2 - - - -
403C ARG* 3.0 33.2 + - - +
404C GLU* 2.8 43.7 + - - +
405C ARG* 3.0 19.9 + - - +
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Residues in contact with GLU 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1602A SO4 4.4 4.3 + - - +
341C PRO* 3.4 43.5 - - + +
360C PRO* 3.9 8.6 - - - +
361C LEU* 3.4 17.7 + - + +
362C SER* 2.8 39.7 + - - -
365C PHE* 3.9 6.6 - - - -
399C VAL* 3.2 6.9 - - + +
400C ASP* 1.3 76.5 - - - +
402C ILE* 1.3 61.7 + - + +
405C ARG* 2.6 58.5 + - - +
406C LEU* 3.4 1.7 + - - -
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Residues in contact with ILE 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A HEM 5.2 0.9 - - + -
336C HIS* 3.5 34.8 - - + +
339C ILE* 4.1 22.7 - - + -
361C LEU* 4.2 14.6 - - + -
365C PHE* 4.0 19.1 - - + -
398C ALA* 4.3 13.5 - - + -
399C VAL* 3.2 20.4 - - + +
401C GLU* 1.3 82.9 - - + +
403C ARG* 1.3 61.3 + - - +
404C GLU 3.6 0.9 - - - -
406C LEU* 3.4 22.1 - - + +
415C LEU 3.6 0.2 - - - +
417C LEU* 2.9 41.6 + - + -
418C PRO* 4.7 2.2 - - + -
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Residues in contact with ARG 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG* 3.1 29.2 + - - +
65A SER* 2.8 43.3 + - - +
66A ASN* 2.6 35.5 + - - +
69A VAL* 4.1 7.9 - - - -
70A ARG* 3.4 52.7 - - - +
135C PRO* 4.3 2.2 - - - +
398C ALA 4.4 3.6 - - - +
399C VAL 2.9 17.4 + - - +
400C ASP* 3.0 20.5 + - - +
402C ILE* 1.3 79.4 - - - +
404C GLU* 1.3 84.6 + - - +
415C LEU 3.7 2.0 - - - +
416C ASP* 3.2 30.8 + - - +
418C PRO* 4.0 11.0 - - + -
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Residues in contact with GLU 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG* 2.7 33.2 + - - -
70A ARG* 5.1 2.1 + - - -
135C PRO* 3.9 13.2 - - - +
136C ARG* 2.8 56.9 + - - +
400C ASP* 2.8 37.6 + - + +
403C ARG* 1.3 93.9 + - - +
405C ARG* 1.3 77.4 + - + +
408C GLU* 3.7 1.9 - - - +
414C GLY* 3.5 6.1 - - - -
415C LEU 3.6 4.0 - - - -
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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