Contacts of the helix formed by residues 416 - 428 (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 ASP 416 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ARG* 2.8 28.7 + - - +
65A SER* 2.7 26.7 + - - -
144C ILE* 3.8 16.4 - - + +
402C ILE 3.8 0.2 - - - -
403C ARG* 3.2 18.8 - - - +
415C LEU* 1.3 74.4 - - - +
417C LEU* 1.3 57.5 + - - +
418C PRO* 3.0 13.2 - - - +
419C ALA* 2.9 35.0 + - + -
420C LEU* 2.8 32.3 + - - +
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Residues in contact with LEU 417 (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 3.4 65.1 - - + -
336C HIS* 3.5 31.0 - - + +
339C ILE* 5.0 0.2 - - + -
402C ILE* 2.9 33.6 + - + +
406C LEU* 3.9 18.3 - - + +
415C LEU 4.0 0.8 - - - -
416C ASP* 1.3 70.5 - - - +
418C PRO* 1.4 63.2 - - + +
420C LEU* 3.1 5.5 + - + +
421C ASN* 2.8 45.6 + - - +
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Residues in contact with PRO 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A SER* 4.0 8.3 - - - +
69A VAL* 3.9 25.8 - - + -
336C HIS* 6.1 1.3 - - + -
398C ALA* 3.9 16.4 - - + -
402C ILE* 4.0 10.3 - - + +
403C ARG* 4.0 9.2 - - + -
416C ASP* 3.0 17.5 - - - +
417C LEU* 1.4 88.0 - - + +
419C ALA* 1.3 61.4 + - - +
421C ASN* 3.3 14.3 + - - +
422C MET* 3.2 27.9 + - - +
477C TRP* 3.8 24.0 - - + -
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Residues in contact with ALA 419 (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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61A ALA* 3.3 34.6 - - - +
62A ARG* 3.9 4.0 - - + +
65A SER* 4.0 0.9 - - - -
128C LEU* 3.6 21.3 - - + -
416C ASP* 2.9 32.3 + - + +
418C PRO* 1.3 73.5 - - - +
420C LEU* 1.3 61.0 + - - +
422C MET* 3.2 5.8 + - - +
423C GLN* 3.0 25.1 + - - +
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Residues in contact with LEU 420 (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 3.9 28.6 - - + +
128C LEU* 4.1 10.5 - - + +
144C ILE* 4.4 5.6 - - + -
145C PRO 3.8 22.9 - - - +
146C PHE* 3.9 20.6 - - + -
406C LEU* 3.8 15.9 - - + -
415C LEU* 3.8 33.9 - - + -
416C ASP 2.8 29.9 + - - +
417C LEU* 3.4 8.1 - - + +
419C ALA* 1.3 74.0 - - - +
421C ASN* 1.3 52.5 + - - +
423C GLN* 3.7 2.5 - - - +
424C ARG* 2.8 36.2 + - - +
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Residues in contact with ASN 421 (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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330C ASN* 2.9 24.6 + - - +
333C ARG* 2.9 41.8 - - - +
336C HIS* 2.8 32.6 + - - +
417C LEU* 2.8 27.6 + - - +
418C PRO* 3.3 11.6 - - - +
420C LEU* 1.3 71.8 - - - +
422C MET* 1.4 56.5 + - - +
424C ARG* 3.4 0.9 + - - +
425C SER* 3.1 13.5 + - - -
477C TRP* 3.6 35.9 + - + -
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Residues in contact with MET 422 (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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61A ALA* 3.8 22.9 - - + +
64A VAL* 3.4 38.6 - - + -
65A SER* 3.9 10.3 - - - +
69A VAL* 4.5 0.2 - - + -
418C PRO* 3.2 26.4 + - + +
419C ALA 3.2 8.1 + - - +
421C ASN* 1.4 74.6 - - - +
423C GLN* 1.3 63.2 + - - +
425C SER* 2.8 22.7 + - - -
426C ARG* 3.3 17.1 + - - +
468C TYR* 3.4 12.1 - - - -
475C ASP* 3.7 21.5 - - + +
477C TRP* 4.4 12.1 - - + -
478C MET* 4.0 21.3 - - + +
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Residues in contact with GLN 423 (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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61A ALA* 4.1 5.0 + - + +
126C PHE* 2.9 55.9 + - + -
127C PRO 3.4 13.3 + - - -
128C LEU* 3.6 34.4 - - + +
129C LYS 5.0 0.2 - - - +
146C PHE* 3.6 18.4 - - + -
419C ALA 3.0 15.6 + - - +
420C LEU 3.8 1.6 - - - +
422C MET* 1.3 77.2 - - - +
424C ARG* 1.3 57.6 + - - +
426C ARG* 3.3 22.3 + - - +
427C ASP* 2.9 25.8 + - - +
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Residues in contact with ARG 424 (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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100A THR* 5.5 1.8 - - - -
102A GLU* 3.0 23.7 + - - -
605A HEM 2.8 37.1 + - - +
146C PHE* 3.2 26.3 - - - +
147C PHE 2.8 26.3 + - - +
149C SER* 3.3 12.6 + - - +
329C THR* 5.9 0.9 - - - +
330C ASN* 4.0 6.1 - - - +
333C ARG* 3.5 21.5 - - - +
420C LEU 2.8 17.2 + - - +
421C ASN 3.6 5.8 - - - +
422C MET 3.2 0.2 - - - -
423C GLN* 1.3 74.9 - - - +
425C SER* 1.3 61.0 + - - +
427C ASP* 2.9 19.6 + - - -
428C HIS* 2.8 63.7 + - + +
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Residues in contact with SER 425 (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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330C ASN* 3.6 25.2 + - - +
421C ASN 3.1 6.8 + - - -
422C MET* 2.8 26.2 + - - -
424C ARG* 1.3 77.3 - - - +
426C ARG* 1.3 57.6 + - - +
428C HIS* 3.2 2.1 + - - -
429C GLY 3.2 3.6 + - - -
430C LEU* 3.0 51.1 + - - +
475C ASP* 3.8 16.3 + - - +
476C ILE* 4.1 8.5 - - - -
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Residues in contact with ARG 426 (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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36A GLU 4.9 0.9 - - - +
37A TYR* 4.2 0.5 - - - -
44A PRO* 3.4 18.5 - - + +
45A TYR* 3.8 35.2 + - + +
46A GLY* 5.7 0.6 - - - -
53A ARG* 5.0 9.1 - - - +
58A VAL* 3.6 18.7 - - - +
59A ALA* 2.7 34.1 + - - +
60A LEU* 4.4 1.0 - - - +
61A ALA* 3.6 22.7 - - - +
64A VAL* 4.7 1.4 - - - +
126C PHE* 4.5 2.0 - - + -
422C MET 3.4 13.7 + - - +
423C GLN* 3.3 22.0 + - - +
424C ARG 3.2 0.6 - - - -
425C SER* 1.3 73.6 + - - +
427C ASP* 1.3 65.4 + - - +
428C HIS 3.0 1.6 - - - -
429C GLY* 2.9 14.9 + - - +
430C LEU 5.0 1.8 - - - +
468C TYR* 4.0 10.5 + - - -
475C ASP* 2.8 40.9 + - - +
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Residues in contact with ASP 427 (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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37A TYR* 3.3 10.0 - - - -
44A PRO* 3.9 12.0 - - - +
126C PHE* 4.6 1.8 - - + -
146C PHE* 3.7 12.6 - - + -
148C ARG* 2.8 59.1 + - - +
149C SER* 2.9 34.2 + - - +
161C ARG* 4.6 1.0 + - - -
163C GLN* 3.6 5.4 + - - -
423C GLN 2.9 14.3 + - - +
424C ARG* 2.9 22.9 + - - +
426C ARG* 1.3 74.2 - - - +
428C HIS* 1.3 63.4 + - - +
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Residues in contact with HIS 428 (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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29A PHE* 4.6 1.8 - + - -
31A ARG* 2.8 33.3 + - - -
37A TYR* 3.7 4.5 - - - -
100A THR* 3.7 19.1 - - + -
149C SER* 2.9 21.4 + - - -
163C GLN* 3.4 30.2 + - + +
326C ASN* 2.7 29.0 + - - +
329C THR* 4.1 14.4 + - - -
333C ARG* 5.8 0.7 - - - -
424C ARG* 2.8 35.9 + - + +
425C SER 3.7 4.7 - - - +
426C ARG 3.0 0.4 - - - -
427C ASP* 1.3 90.5 - - - +
429C GLY* 1.3 58.0 + - - +
430C LEU* 3.2 9.3 + - + +
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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