Contacts of the helix formed by residues 475 - 483 (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 475 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ARG* 4.6 8.3 + - - +
422C MET* 3.7 22.5 - - + +
425C SER* 3.8 14.9 + - - +
426C ARG* 2.8 48.8 + - - +
432C GLY* 5.3 1.8 - - - -
468C TYR* 2.7 25.9 + - - +
473C ASN 3.2 4.7 + - - +
474C ILE* 1.4 75.5 - - - +
476C ILE* 1.3 68.0 + - - +
477C TRP 4.6 2.2 - - - +
478C MET* 3.0 4.5 + - + +
479C GLY* 2.9 21.1 + - - -
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Residues in contact with ILE 476 (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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327C VAL* 3.9 18.4 - - + -
330C ASN* 3.4 27.6 - - + +
331C ALA* 4.8 8.3 - - + +
425C SER* 4.1 11.6 + - - -
430C LEU* 4.2 12.1 - - + -
431C PRO 4.5 6.2 + - - +
433C TYR* 5.1 6.3 - - - +
436C TRP* 3.8 31.2 - - + -
474C ILE 3.6 2.9 + - - -
475C ASP* 1.3 70.7 - - - +
477C TRP* 1.4 61.1 + - - +
479C GLY 4.7 0.2 - - - +
480C GLY* 2.8 29.1 + - - +
494C LEU* 3.6 29.2 - - + -
495C LEU* 4.8 2.4 - - + +
498C ILE* 3.9 11.4 - - + -
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Residues in contact with TRP 477 (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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69A VAL* 4.2 2.0 - - + -
330C ASN* 3.4 22.6 + - - +
331C ALA* 5.1 3.8 - - - +
333C ARG* 2.9 47.0 + - + -
334C TYR* 4.0 2.2 - - - +
336C HIS* 4.7 7.0 - - + -
337C THR* 3.8 20.4 - - + -
397C ILE* 3.8 19.3 - - + -
398C ALA* 4.7 2.0 - - + -
418C PRO* 3.8 42.2 - - + -
421C ASN* 3.6 25.6 + - + -
422C MET* 4.4 6.3 - - + -
475C ASP* 3.3 1.6 - - - +
476C ILE* 1.4 82.2 - - - +
478C MET* 1.3 91.3 + - + +
480C GLY* 5.0 0.2 - - - -
481C VAL* 2.9 49.7 + - + +
495C LEU* 5.6 2.2 - - + -
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Residues in contact with MET 478 (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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64A VAL* 3.6 23.1 - - + -
68A ILE* 3.5 25.1 - - + -
69A VAL* 3.9 21.3 - - + -
397C ILE* 3.8 15.5 - - + -
422C MET* 4.0 14.6 - - - +
464C LEU* 4.1 16.6 - - + -
468C TYR* 3.5 24.7 - - + +
474C ILE* 4.1 0.9 - - + -
475C ASP* 3.0 9.1 + - - +
477C TRP* 1.3 85.6 - - + +
479C GLY* 1.3 62.0 + - - +
481C VAL* 3.7 8.5 - - + +
482C SER* 2.9 36.5 + - - +
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Residues in contact with GLY 479 (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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433C TYR* 3.6 28.2 - - - -
455C LEU* 4.9 0.6 - - - +
464C LEU* 5.6 1.3 - - - -
474C ILE* 3.5 15.3 - - - +
475C ASP 2.9 11.8 + - - -
478C MET* 1.3 75.7 - - - +
480C GLY* 1.4 63.6 + - - +
482C SER* 3.2 16.9 + - - -
483C GLU* 3.4 17.0 + - - +
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Residues in contact with GLY 480 (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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433C TYR* 4.5 2.0 - - - -
476C ILE 2.8 21.7 + - - -
477C TRP 3.7 0.7 - - - -
479C GLY* 1.4 74.6 - - - +
481C VAL* 1.3 59.5 + - - +
482C SER 3.3 0.2 + - - -
483C GLU* 3.5 18.5 + - - +
492C GLY 4.8 2.3 + - - -
494C LEU* 4.6 11.2 - - - -
495C LEU* 3.3 36.1 - - - +
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Residues in contact with VAL 481 (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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334C TYR* 4.0 15.0 - - + -
337C THR* 3.8 19.5 - - + -
392C ASN* 3.2 26.1 + - - +
393C ARG 6.0 0.2 - - - -
394C GLN* 5.5 2.3 - - - +
397C ILE* 3.8 28.5 - - + +
477C TRP* 2.9 62.3 + - + +
478C MET* 3.7 9.2 - - + +
480C GLY* 1.3 72.4 - - - +
482C SER* 1.3 61.9 + - - +
483C GLU 3.3 3.8 + - - +
485C LEU* 6.1 0.4 - - - -
495C LEU* 4.1 9.4 - - + -
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Residues in contact with SER 482 (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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394C GLN* 2.8 37.6 + - - +
397C ILE* 4.4 6.7 - - - +
455C LEU* 3.9 9.5 - - - +
460C LEU* 3.7 22.9 - - - +
464C LEU* 4.2 15.8 - - - +
478C MET* 2.9 35.3 + - - +
479C GLY* 3.2 8.9 + - - -
481C VAL* 1.3 77.6 - - - +
483C GLU* 1.4 56.6 + - - +
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Residues in contact with GLU 483 (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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394C GLN* 5.2 1.2 - - - +
433C TYR* 2.6 35.0 + - - +
437C ARG* 2.8 23.5 + - - -
454C VAL* 5.0 3.1 - - + -
455C LEU* 3.8 8.3 - - + -
479C GLY 3.4 13.2 + - - +
480C GLY 3.8 9.7 - - - +
481C VAL 3.3 6.2 - - - +
482C SER* 1.4 80.2 - - - +
484C PRO* 1.4 74.3 - - + +
485C LEU* 3.5 14.0 + - - +
492C GLY* 3.7 9.6 + - - -
493C PRO* 3.2 13.0 - - + +
494C LEU* 2.8 36.3 + - - +
495C LEU 4.5 0.3 + - - -
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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