Contacts of the helix formed by residues 84 - 98 (chain A) 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 LEU 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A SER* 1.3 72.5 - - - +
85A MET* 1.4 56.4 + - - +
86A PHE 3.1 0.2 - - - -
87A MET* 3.0 33.9 + - + +
88A GLN* 2.9 25.3 + - - +
245C GLU* 6.1 1.3 - - + +
338C LEU 4.1 4.3 - - - +
340C GLN* 4.0 22.2 - - + +
342C PHE 4.6 4.0 - - - +
343C MET* 6.0 0.2 - - - -
344C PHE* 3.8 35.0 - - + +
383C GLY 4.5 2.7 - - - +
384C LEU* 3.3 28.2 + - + +
387C THR* 2.7 25.8 + - + +
388C PRO 4.1 0.7 - - - +
389C ALA* 3.5 19.4 - - - +
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Residues in contact with MET 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A SER* 3.0 13.0 - - - +
84A LEU* 1.4 74.7 - - - +
86A PHE* 1.3 56.2 + - - +
88A GLN* 4.2 4.5 - - - +
89A TRP* 2.8 34.5 + - - +
249C MET* 3.6 41.7 - - + +
381C LEU* 4.0 11.2 - - + +
384C LEU* 3.0 40.2 + - + +
385C MET* 4.3 11.2 - - + +
533C LEU* 4.2 3.1 - - + -
537C ILE* 4.2 16.8 - - + -
551C ILE* 4.1 19.5 - - + +
552C PHE* 3.8 15.9 - - + -
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Residues in contact with PHE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ARG* 3.7 37.5 - - + -
83A SER* 3.0 17.9 + - - +
85A MET* 1.3 75.8 - - - +
87A MET* 1.3 65.3 + - - +
90A GLY* 3.5 2.8 + - - -
296C TYR* 3.3 38.3 + + - -
299C LEU* 3.8 19.5 - - + -
300C VAL* 3.7 22.0 - - + -
334C TYR* 3.8 13.5 - - - -
338C LEU* 3.7 32.7 - - + +
389C ALA* 4.9 1.8 - - + -
490C ARG* 3.8 22.9 - - + -
552C PHE* 3.6 33.6 - - + +
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Residues in contact with MET 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A SER 3.8 0.6 + - - -
84A LEU* 3.0 40.2 + - + +
86A PHE* 1.3 81.6 - - - +
88A GLN* 1.3 95.8 + - + +
90A GLY* 3.2 8.5 + - - -
605A HEM 3.2 43.6 - - + +
243C MET* 4.1 17.0 - - + -
245C GLU* 5.4 1.1 - - + +
338C LEU* 3.9 35.2 - - + +
339C ILE* 3.9 28.9 - - + +
340C GLN 5.7 0.2 - - - +
384C LEU* 4.8 2.9 - - + -
389C ALA* 4.8 1.7 - - + +
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Residues in contact with GLN 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU 2.9 14.4 + - - +
85A MET* 3.2 5.4 + - - +
87A MET* 1.3 93.4 - - + +
89A TRP* 1.3 62.1 + - - +
91A GLN* 2.8 27.1 + - - +
92A LEU* 3.0 20.7 + - - +
243C MET* 3.4 9.9 - - - +
245C GLU* 3.3 33.2 - - - +
246C LEU* 3.3 28.8 - - - +
249C MET* 3.8 14.8 - - + -
384C LEU* 3.9 19.1 - - + -
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Residues in contact with TRP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A MET* 2.8 13.3 + - + +
86A PHE 4.3 0.2 - - - +
88A GLN* 1.3 70.8 - - - +
90A GLY* 1.4 53.5 + - - +
92A LEU* 3.2 26.7 + - + +
93A LEU* 2.7 41.8 + - + +
175C MET* 5.8 0.2 - - + -
249C MET* 3.7 27.4 - - + -
253C LEU* 5.1 8.5 - - + -
288C VAL* 3.8 29.8 - - + -
291C ILE* 3.7 33.9 - - + -
292C THR* 2.9 31.5 + - - +
296C TYR* 3.7 31.2 - + + -
533C LEU* 3.8 20.4 - - + -
552C PHE* 3.4 26.7 - + + -
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Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PHE 3.5 4.6 + - - -
87A MET 3.2 4.7 + - - -
88A GLN 3.2 0.4 - - - -
89A TRP* 1.4 79.0 - - - +
91A GLN* 1.3 55.8 + - - +
93A LEU* 4.4 2.7 - - - -
94A ASP* 2.8 29.5 + - - +
605A HEM 3.6 15.7 - - - -
296C TYR* 3.3 29.5 - - - -
332C PHE* 3.4 6.9 - - - -
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Residues in contact with GLN 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A MET* 3.3 5.0 + - - +
88A GLN* 2.8 34.0 + - - +
90A GLY* 1.3 76.6 - - - +
92A LEU* 1.3 61.9 + - - +
94A ASP* 3.2 2.3 + - - +
95A HIS* 3.1 43.4 + - + +
605A HEM 3.2 32.5 - - + +
1844A CYN 3.2 28.6 + - - -
242C GLU* 2.8 26.5 + - - -
243C MET* 3.5 15.9 - - - +
246C LEU* 3.6 18.5 - - + +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLN 3.0 13.9 + - - +
89A TRP* 3.5 40.4 - - + +
91A GLN* 1.3 75.9 - - - +
93A LEU* 1.3 60.4 + - - +
95A HIS* 3.2 14.6 + - - +
96A ASP 3.3 8.1 + - - -
175C MET* 3.6 32.2 - - + +
246C LEU* 3.9 21.0 - - + +
249C MET* 3.8 31.9 - - + +
250C HIS* 4.1 17.3 - - + +
253C LEU* 4.0 17.3 - - + -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A TRP* 2.7 27.8 + - + +
90A GLY 3.7 3.8 - - - +
92A LEU* 1.3 72.1 - - - +
94A ASP* 1.4 65.7 + - - +
95A HIS 3.1 0.2 - - - -
96A ASP* 3.0 24.5 + - + +
97A LEU* 3.3 24.7 + - + +
171C VAL* 4.4 13.7 - - + -
175C MET* 4.8 3.1 - - - -
288C VAL* 4.6 4.0 - - + -
292C THR* 3.5 41.7 - - + +
296C TYR* 4.0 21.5 - - + -
332C PHE* 4.2 4.0 - - + -
503C PHE* 3.6 25.6 - - + -
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLY 2.8 19.3 + - - +
91A GLN 3.4 7.4 - - - +
93A LEU* 1.4 75.3 - - - +
95A HIS* 1.4 67.4 + - + +
97A LEU* 2.9 8.6 + - - +
98A ASP* 2.9 36.0 + - - +
605A HEM 1.6 76.7 - - + +
239C ARG* 3.7 0.2 + - - -
332C PHE* 3.4 16.2 - - + -
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Residues in contact with HIS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLN* 3.1 23.8 + - + +
92A LEU* 3.5 11.7 - - - +
93A LEU 3.1 0.8 - - - -
94A ASP* 1.4 80.1 - - + +
96A ASP* 1.3 58.5 + - - +
97A LEU 3.4 0.2 - - - -
1844A CYN 3.0 24.6 + - - -
167C LEU* 3.2 18.2 - - - +
174C SER* 4.8 0.5 + - - -
175C MET* 3.5 19.8 + - + +
237C ASP* 3.4 21.2 + - + +
239C ARG* 3.2 47.8 + - + +
242C GLU* 5.3 0.4 - - + -
246C LEU* 3.4 37.0 - - + +
250C HIS* 4.6 4.6 + - - +
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Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU 3.3 2.2 + - - -
93A LEU* 3.0 16.4 + - + +
95A HIS* 1.3 77.8 - - - +
97A LEU* 1.4 55.6 + - + +
167C LEU* 4.2 2.6 - - - +
168C THR 2.8 11.1 - - - +
170C PHE 3.1 2.8 - - - +
171C VAL* 3.9 4.8 - - - +
172C ASP* 2.8 18.0 + - - +
173C ALA* 2.9 28.2 + - - -
174C SER* 3.2 10.1 + - - -
175C MET* 3.7 19.3 - - + +
288C VAL* 3.7 16.1 - - - +
1600C CA 2.4 53.6 - - - -
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.3 22.7 - - + +
94A ASP* 2.9 8.3 + - - +
96A ASP* 1.4 84.8 - - + +
98A ASP* 1.4 67.8 + - - +
165C ASN* 2.7 21.8 + - - +
167C LEU* 4.1 2.4 - - - +
168C THR 3.8 8.9 - - - +
169C SER 3.2 20.4 - - - +
170C PHE 4.2 2.0 - - - +
171C VAL* 3.8 17.5 - - + -
324C ILE* 3.4 14.2 - - + +
328C PHE* 3.7 19.5 - - + -
332C PHE* 5.2 0.4 - - + -
503C PHE* 3.6 33.9 - - + -
506C LEU* 3.7 15.7 - - + -
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Residues in contact with ASP 98 (chain A).
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* 4.1 2.7 - - + -
94A ASP* 2.9 24.9 + - - +
97A LEU* 1.4 87.6 - - - +
99A PHE* 1.3 57.8 + - - +
605A HEM 2.8 35.3 - - - +
165C ASN* 3.3 15.5 - - - +
167C LEU* 3.3 7.3 - - - +
239C ARG* 3.0 22.7 + - - -
324C ILE* 4.2 3.5 - - + +
328C PHE* 3.6 17.8 - - - -
329C THR* 3.4 31.3 - - + +
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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
------------------------------------------------------------
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