Contacts of the helix formed by residues 78 - 90 (chain D) in PDB entry 3GZN
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 GLY 78 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D GLY 3.4 4.9 + - - -
77D ALA* 1.3 78.7 - - - +
79D GLY* 1.3 61.3 + - - +
80D LEU 3.5 1.8 - - - -
81D GLY* 3.8 2.2 - - - +
82D CYS* 2.9 29.5 + - - +
100D ASP* 3.7 2.2 + - - -
112D GLN* 3.4 17.4 - - - +
124D LYS* 4.2 0.2 - - - -
76J GLY 4.3 0.4 - - - -
464J B39 3.1 26.4 + - - -
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Residues in contact with GLY 79 (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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78D GLY* 1.3 72.0 - - - +
80D LEU* 1.3 63.5 + - - +
82D CYS* 4.1 2.1 - - - +
83D GLU* 3.5 18.9 + - - +
111D ARG* 4.5 10.3 - - - +
112D GLN* 3.5 16.8 - - - +
113D PHE* 5.5 0.5 - - - -
317D ASN* 4.1 24.7 - - - +
76J GLY 3.8 1.3 - - - -
464J B39 2.7 16.1 + - - -
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLY* 1.3 75.1 - - - +
81D GLY* 1.3 56.7 + - - +
83D GLU* 3.2 5.0 + - - +
84D LEU* 2.8 37.2 + - + +
165D GLY* 3.8 16.4 - - - -
201D GLY* 3.4 34.1 - - - +
202D GLY* 3.8 5.2 - - - +
203D THR* 4.4 1.1 - - + -
317D ASN* 3.5 36.1 + - - +
320D ILE* 3.5 25.4 - - + -
321D ALA* 3.7 13.1 - - + +
324D CYS* 5.5 1.3 - - - -
75J GLY 4.3 0.2 - - - +
76J GLY* 3.0 30.4 + - - +
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Residues in contact with GLY 81 (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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74D VAL* 4.2 1.4 - - - +
75D ILE 5.3 1.1 - - - -
76D GLY 3.0 29.3 - - - -
77D ALA* 4.5 2.7 - - - -
78D GLY* 3.5 6.8 + - - +
79D GLY 3.3 1.0 - - - -
80D LEU* 1.3 78.0 - - - +
82D CYS* 1.3 61.8 + - - +
84D LEU* 3.1 14.4 + - - +
85D LEU* 3.0 28.5 + - - +
165D GLY* 4.9 2.4 + - - -
76J GLY 4.5 0.8 + - - -
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Residues in contact with CYS 82 (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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77D ALA* 3.4 16.9 - - - -
78D GLY 2.9 26.8 + - - +
79D GLY 4.1 2.7 - - - +
81D GLY* 1.3 71.0 - - - +
83D GLU* 1.3 62.2 + - - +
85D LEU* 3.5 6.5 + - - +
86D LYS* 3.2 17.8 + - - +
112D GLN* 4.3 8.7 - - - -
113D PHE* 3.6 24.0 - - + +
114D LEU* 3.7 40.5 - - + +
115D PHE* 4.0 18.8 - - - -
128D ALA* 4.9 1.1 - - - -
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Residues in contact with GLU 83 (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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51C GLU* 3.7 3.1 - - - +
54C LYS* 2.8 40.5 + - - -
502C ALA* 5.1 1.1 - - + +
79D GLY 3.5 11.0 + - - +
80D LEU 3.2 4.4 + - - +
82D CYS* 1.3 77.3 - - - +
84D LEU* 1.3 58.2 + - - +
86D LYS* 3.1 18.3 + - - +
87D ASN* 2.9 43.1 + - - +
111D ARG 5.1 2.1 - - - +
113D PHE* 3.6 15.9 - - - -
314D ALA* 4.5 3.5 - - - +
317D ASN* 4.5 3.0 - - - +
318D ALA* 3.7 26.0 + - - +
321D ALA* 3.4 23.8 - - + -
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Residues in contact with LEU 84 (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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74D VAL* 4.1 25.6 - - + -
80D LEU* 2.8 26.0 + - + +
81D GLY* 3.1 11.6 + - - +
83D GLU* 1.3 72.7 - - - +
85D LEU* 1.3 52.3 + - - +
87D ASN* 3.1 5.5 + - - +
88D LEU* 2.8 44.3 + - + +
163D VAL* 3.9 24.5 - - + -
164D CYS 4.3 2.2 - - - +
165D GLY* 4.3 17.3 - - - +
321D ALA* 3.5 28.0 - - + +
324D CYS* 3.7 22.2 - - + -
325D ALA* 4.3 5.8 - - + +
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Residues in contact with LEU 85 (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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74D VAL* 4.4 5.4 - - + -
77D ALA* 5.1 3.4 - - + -
81D GLY 3.0 17.3 + - - +
82D CYS* 3.5 9.0 - - - +
84D LEU* 1.3 76.0 - - - +
86D LYS* 1.3 62.5 + - - +
88D LEU* 4.0 5.1 - - - +
89D ALA* 3.1 19.2 + - - +
96D ILE* 3.8 25.2 - - + +
98D VAL* 3.4 35.0 - - + -
114D LEU* 4.1 9.9 - - + -
128D ALA* 3.8 29.8 - - + +
132D LEU* 3.3 28.4 - - + +
141D VAL* 3.9 13.0 - - + -
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Residues in contact with LYS 86 (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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51C GLU* 3.0 22.6 + - - +
54C LYS* 4.2 4.7 - - + +
81C PHE* 3.5 51.8 - - + -
498C HIS* 2.8 30.2 + - - +
502C ALA* 3.9 3.0 - - - +
82D CYS 3.2 10.0 + - - +
83D GLU* 3.1 30.3 + - - +
85D LEU* 1.3 77.8 - - - +
87D ASN* 1.3 80.6 + - - +
89D ALA* 3.5 0.7 + - - +
90D LEU* 3.1 27.5 + - + +
113D PHE* 3.7 20.2 - - + -
114D LEU* 5.6 0.8 - - + +
132D LEU* 4.0 4.4 - - - +
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Residues in contact with ASN 87 (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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498C HIS* 3.3 15.3 - - - -
499C THR* 3.8 7.8 - - + +
502C ALA* 3.7 6.1 - - - +
83D GLU* 2.9 33.3 + - - +
84D LEU 3.1 3.6 + - - +
86D LYS* 1.3 101.7 + - - +
88D LEU* 1.3 55.2 + - - +
90D LEU* 3.9 2.3 + - - +
91D SER* 2.6 32.7 + - - -
321D ALA 3.4 29.1 + - - -
322D ALA* 3.5 8.9 - - - +
325D ALA* 3.4 21.0 - - + +
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Residues in contact with LEU 88 (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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72D VAL* 4.0 14.4 - - + -
74D VAL* 3.5 33.0 - - + -
84D LEU* 2.8 21.5 + - + +
85D LEU* 4.1 1.1 - - - +
87D ASN* 1.3 74.1 - - - +
89D ALA* 1.3 60.2 + - - +
90D LEU 3.1 1.8 - - - -
91D SER* 2.8 20.4 + - - -
92D GLY 3.4 0.3 + - - -
93D PHE* 3.2 38.8 + - + +
96D ILE* 3.9 17.0 - - + -
163D VAL* 4.3 6.5 - - + -
325D ALA* 4.4 13.7 - - + +
328D VAL* 3.8 36.6 - - + -
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Residues in contact with ALA 89 (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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38D TRP* 3.5 19.9 - - - -
85D LEU 3.1 18.8 + - - +
86D LYS 3.9 3.6 - - - +
88D LEU* 1.3 75.5 - - - +
90D LEU* 1.3 61.0 + - - +
91D SER 3.5 0.5 + - - -
92D GLY 3.8 1.9 + - - -
93D PHE 3.7 14.9 - - - +
96D ILE* 4.0 3.0 - - + +
132D LEU* 4.0 13.2 - - + -
136D VAL* 4.0 20.3 - - + +
139D CYS* 3.9 23.1 - - - -
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Residues in contact with LEU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ALA 5.2 1.8 - - - +
78C GLY 3.5 25.2 - - - +
79C ASN* 4.1 5.7 - - - +
80C ASN 4.3 9.2 - - - +
81C PHE* 4.0 23.8 - - + +
498C HIS* 3.4 55.7 + - + +
38D TRP* 3.8 14.1 - - + -
41D VAL* 4.1 8.5 - - - +
86D LYS 3.1 16.0 + - - +
87D ASN 4.4 0.4 - - - +
88D LEU 3.1 1.0 - - - -
89D ALA* 1.3 78.0 - - - +
91D SER* 1.3 59.8 + - - +
92D GLY 3.5 0.9 - - - -
136D VAL* 3.8 27.8 - - + -
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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