Contacts of the helix formed by residues 416 - 428 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B ARG* 2.7 27.6 + - - +
65B SER* 2.8 28.4 + - - -
144D ILE* 4.0 14.4 - - + +
402D ILE 3.6 0.4 - - - -
403D ARG* 3.0 21.0 - - - +
406D LEU* 4.4 0.2 - - - -
415D LEU* 1.3 76.6 - - - +
417D LEU* 1.3 50.7 + - - +
418D PRO* 3.1 10.4 - - - +
419D ALA* 2.9 32.1 + - + +
420D LEU* 2.8 37.6 + - - +
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Residues in contact with LEU 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B HEM 3.5 55.4 - - + -
336D HIS* 3.4 41.7 - - + +
339D ILE* 4.6 1.8 - - + -
402D ILE* 2.8 37.1 + - + +
406D LEU* 3.8 13.9 - - + +
416D ASP* 1.3 70.3 - - - +
418D PRO* 1.4 64.8 - - + +
420D LEU* 3.0 3.2 + - - +
421D ASN* 2.8 48.0 + - - +
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Residues in contact with PRO 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B SER* 3.9 8.7 - - - +
69B VAL* 3.8 25.8 - - + -
336D HIS* 5.9 1.1 - - + -
398D ALA* 3.9 15.5 - - + -
402D ILE* 4.1 6.7 - - + +
403D ARG* 4.0 10.1 - - + -
416D ASP* 3.1 12.3 - - - +
417D LEU* 1.4 93.2 - - + +
419D ALA* 1.3 59.7 + - - +
421D ASN* 3.3 9.3 + - - +
422D MET* 3.2 29.8 + - + +
477D TRP* 3.7 30.0 - - + -
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Residues in contact with ALA 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ALA* 3.4 32.4 - - - +
62B ARG* 4.0 4.5 - - + -
65B SER* 4.0 1.5 + - - -
128D LEU* 3.6 18.8 - - + -
416D ASP* 2.9 35.2 + - + +
418D PRO* 1.3 75.8 - - - +
420D LEU* 1.3 65.8 + - - +
422D MET* 3.2 3.7 + - - -
423D GLN* 3.0 21.0 + - - +
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Residues in contact with LEU 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B HEM 3.7 32.3 - - + +
128D LEU* 4.1 8.5 - - + -
144D ILE* 4.1 9.9 - - + -
145D PRO 3.9 22.0 - - - +
146D PHE* 3.9 18.7 - - + -
406D LEU* 3.8 28.7 - - + -
415D LEU* 3.9 19.3 - - + -
416D ASP 2.8 23.1 + - - +
417D LEU* 3.5 6.5 - - - +
419D ALA* 1.3 72.7 - - - +
421D ASN* 1.4 53.3 + - - +
423D GLN* 3.3 5.2 + - - +
424D ARG* 2.7 37.5 + - - +
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Residues in contact with ASN 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D ASN* 2.8 24.8 + - - +
333D ARG* 2.9 41.8 - - - +
336D HIS* 2.8 22.0 + - - -
417D LEU* 2.8 33.5 + - - +
418D PRO* 3.4 9.2 - - - +
420D LEU* 1.4 76.1 - - - +
422D MET* 1.4 56.5 + - - +
424D ARG 3.4 0.3 + - - -
425D SER* 3.1 13.5 + - - -
477D TRP* 3.6 36.3 + - + -
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Residues in contact with MET 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ALA* 3.7 29.6 - - + +
64B VAL* 3.7 16.6 - - + -
65B SER* 3.9 17.5 - - - +
69B VAL* 4.5 2.9 - - + -
330D ASN* 5.5 0.2 - - - -
418D PRO 3.2 25.3 + - - +
419D ALA* 3.8 4.5 - - - +
421D ASN* 1.4 72.9 - - - +
423D GLN* 1.3 64.6 + - - +
425D SER* 3.0 21.5 + - - -
426D ARG* 3.1 19.5 + - - +
468D TYR* 3.4 23.6 - - - -
475D ASP* 3.7 21.5 - - + +
477D TRP* 4.5 9.2 - - + -
478D MET* 3.9 22.9 - - + +
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Residues in contact with GLN 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ALA* 4.1 6.1 + - + +
126D PHE* 3.2 53.2 + - + -
127D PRO 3.5 14.1 + - - -
128D LEU* 3.4 31.9 - - + +
146D PHE* 3.6 20.4 - - + -
419D ALA 3.0 16.9 + - - +
420D LEU 3.6 0.9 - - - +
422D MET* 1.3 74.9 - - - +
424D ARG* 1.3 57.2 + - - +
426D ARG* 3.4 22.6 + - - +
427D ASP* 2.9 28.8 + - - +
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Residues in contact with ARG 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B THR* 6.0 1.1 - - - -
102B GLU* 3.1 23.6 + - - -
605B HEM 2.8 35.2 + - - +
146D PHE* 3.2 24.2 - - - +
147D PHE 2.8 27.5 + - - +
149D SER* 3.0 18.2 + - - +
329D THR* 5.9 0.7 - - - +
330D ASN* 3.9 5.8 - - - +
333D ARG* 3.3 24.6 - - - +
420D LEU 2.7 19.7 + - - +
421D ASN 3.5 5.8 - - - +
422D MET 3.2 0.2 - - - -
423D GLN* 1.3 73.6 - - - +
425D SER* 1.3 57.9 + - - +
427D ASP* 3.0 11.3 + - - -
428D HIS* 2.9 65.4 + - + +
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Residues in contact with SER 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D ASN* 3.6 26.5 + - - +
421D ASN 3.1 9.6 + - - -
422D MET* 3.0 22.5 + - - -
424D ARG* 1.3 75.3 - - - +
426D ARG* 1.3 58.7 + - - +
428D HIS* 3.6 0.6 + - - -
429D GLY 3.3 2.3 + - - -
430D LEU* 2.9 53.3 + - - +
475D ASP* 4.0 16.3 + - - +
476D ILE* 3.9 9.1 + - - +
477D TRP 5.2 0.2 + - - -
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Residues in contact with ARG 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLU 5.0 1.3 - - - +
37B TYR* 4.2 0.2 - - - -
44B PRO* 3.4 18.4 - - + +
45B TYR* 3.8 36.9 + - + +
46B GLY* 5.5 1.2 - - - -
53B ARG* 5.1 6.0 - - - +
58B VAL* 3.6 17.1 - - - +
59B ALA 2.8 30.7 + - - +
60B LEU* 4.5 1.2 - - - +
61B ALA* 3.7 23.7 - - - +
64B VAL* 4.6 1.6 - - - +
126D PHE* 4.6 1.3 - - + -
422D MET 3.1 14.5 + - - +
423D GLN* 3.7 20.5 + - - +
424D ARG 3.2 0.2 - - - -
425D SER* 1.3 75.0 - - - +
427D ASP* 1.3 65.7 + - - +
428D HIS 3.1 1.3 - - - -
429D GLY* 2.9 14.6 + - - +
430D LEU 4.9 1.8 - - - +
468D TYR* 4.2 9.5 + - - -
475D ASP* 2.7 42.6 + - - +
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Residues in contact with ASP 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 3.3 8.7 - - - -
44B PRO* 3.9 12.0 - - - +
126D PHE* 4.5 2.9 - - + -
146D PHE* 3.8 12.1 - - + -
148D ARG* 2.8 52.5 + - - +
149D SER* 2.7 36.3 + - - +
161D ARG* 4.7 0.9 + - - -
163D GLN* 3.6 5.0 + - - -
423D GLN 2.9 14.8 + - - +
424D ARG* 3.0 22.0 + - - +
426D ARG* 1.3 75.7 - - - +
428D HIS* 1.3 62.5 - - - +
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Residues in contact with HIS 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PHE* 4.8 1.6 - + - -
31B ARG* 2.8 31.9 + - - -
37B TYR* 3.6 4.5 - - - -
100B THR* 3.6 20.6 - - + -
149D SER* 2.7 22.2 + - - -
163D GLN* 3.5 30.4 + - + +
326D ASN* 2.9 27.9 + - - +
329D THR* 4.0 14.2 + - - -
333D ARG* 5.7 0.9 - - - -
424D ARG* 2.9 33.8 + - + +
425D SER* 4.0 0.4 - - - +
426D ARG 3.1 0.4 - - - -
427D ASP* 1.3 90.0 - - - +
429D GLY* 1.3 58.9 + - - +
430D LEU* 3.2 13.3 + - + +
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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