Contacts of the helix formed by residues 83 - 102 (chain D) in PDB entry 4GCK
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 83 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D GLU* 2.8 14.5 + - - +
82D LYS* 1.3 80.7 - - + +
84D THR* 1.3 59.5 + - - +
85D THR* 3.3 12.6 + - - -
86D ALA* 2.9 31.0 + - + +
87D ARG* 2.9 32.4 + - - +
147D GLU* 3.5 17.6 - - - +
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Residues in contact with THR 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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82D LYS 3.5 1.0 + - - -
83D ASP* 1.3 71.4 - - - +
85D THR* 1.3 63.8 + - - +
87D ARG* 3.1 13.8 + - - +
88D LEU* 3.1 25.1 + - + +
139D VAL* 3.8 29.0 + - + +
143D LYS* 3.7 23.6 + - + -
146D ARG* 4.3 10.9 - - - -
147D GLU* 3.0 30.0 + - - -
151D TYR* 3.4 24.9 - - + +
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Residues in contact with THR 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ASP* 3.3 10.0 + - - -
84D THR* 1.3 78.6 - - - +
86D ALA* 1.3 61.6 + - - +
88D LEU* 3.4 9.3 + - - +
89D ARG* 3.1 22.4 + - - +
143D LYS* 4.1 15.6 + - - -
147D GLU* 5.2 0.7 + - - -
151D TYR* 4.4 4.3 + - - -
190D TRP* 3.9 23.1 - - + +
194D ALA* 4.7 9.2 - - + -
197D LEU* 4.9 7.4 - - + +
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Residues in contact with ALA 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D GLU* 3.4 32.8 - - + +
83D ASP* 2.9 21.9 + - + +
84D THR 3.2 0.2 - - - -
85D THR* 1.3 76.7 - - - +
87D ARG* 1.3 62.3 + - - +
89D ARG* 3.5 9.6 + - - +
90D LEU* 3.1 30.6 + - + +
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Residues in contact with ARG 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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77D ILE* 4.2 7.8 - - + +
78D LEU* 2.9 55.6 + - + +
81D GLU* 2.6 32.6 + - + +
82D LYS* 4.0 3.9 + - - +
83D ASP 2.9 29.2 + - - +
84D THR* 3.1 12.7 + - - +
86D ALA* 1.3 75.7 - - - +
88D LEU* 1.3 65.4 + - - +
90D LEU* 3.5 1.6 + - - +
91D ILE* 3.0 31.6 + - - +
138D GLN* 4.9 2.8 + - - -
139D VAL* 3.9 23.4 + - + +
142D GLU* 3.9 5.5 + - - -
146D ARG* 3.5 47.2 - - - +
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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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84D THR* 3.1 17.2 + - + +
85D THR* 3.8 7.2 - - - +
87D ARG* 1.3 72.5 - - - +
89D ARG* 1.3 66.5 + - - +
91D ILE* 3.3 5.0 + - + +
92D VAL* 3.0 28.4 + - - +
136D LEU* 3.8 35.8 - - + +
139D VAL* 3.7 19.7 - - + -
140D MET* 4.0 20.6 - - + -
151D TYR* 3.5 24.9 - - - +
162D LEU* 4.3 4.5 - - + -
190D TRP* 3.8 14.4 - - + -
197D LEU* 3.5 19.1 - - + -
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Residues in contact with ARG 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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85D THR 3.1 17.5 + - - +
86D ALA* 3.6 8.7 - - - +
88D LEU* 1.3 76.7 - - - +
90D LEU* 1.3 80.1 + - - +
92D VAL* 3.7 0.5 - - - +
93D LEU* 2.8 37.9 + - - +
186D PHE* 3.7 20.4 - - + -
187D GLU* 2.8 29.3 + - - -
190D TRP* 3.4 49.7 - - + +
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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
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77D ILE* 3.5 33.6 - - + +
81D GLU* 4.1 27.8 - - + +
86D ALA* 3.1 18.7 + - + +
87D ARG 4.0 2.9 - - - +
89D ARG* 1.3 96.1 - - - +
91D ILE* 1.3 61.9 + - - +
93D LEU* 3.7 15.9 - - + +
94D LEU* 2.8 31.8 + - - +
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Residues in contact with ILE 91 (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 ILE* 3.4 48.9 - - + -
77D ILE* 4.3 10.1 - - + -
78D LEU* 4.4 7.2 - - + -
87D ARG 3.0 25.7 + - - +
88D LEU* 3.8 4.0 - - - +
89D ARG 3.3 0.4 - - - -
90D LEU* 1.3 75.0 - - - +
92D VAL* 1.3 59.1 + - + +
94D LEU* 3.3 3.3 + - - +
95D ILE* 3.0 42.2 + - + +
132D ILE* 4.9 3.8 - - + -
135D GLN* 5.5 5.2 - - + -
136D LEU* 3.7 31.0 - - + -
139D VAL* 4.4 20.6 - - + -
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Residues in contact with VAL 92 (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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88D LEU 3.0 18.6 + - - +
89D ARG 3.7 2.9 - - - +
91D ILE* 1.3 75.9 - - + +
93D LEU* 1.3 67.9 + - - +
95D ILE* 3.2 3.8 + - + +
96D LEU* 3.0 25.2 + - + +
136D LEU* 5.3 4.9 - - + -
162D LEU* 4.2 22.2 - - + +
165D PHE* 3.8 30.1 - - + -
166D CYS* 3.9 24.5 - - - -
186D PHE* 3.9 13.0 - - + -
190D TRP* 4.0 17.9 - - + -
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Residues in contact with LEU 93 (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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89D ARG* 2.8 30.1 + - - +
90D LEU* 3.7 22.0 - - + +
92D VAL* 1.3 73.0 - - - +
94D LEU* 1.3 52.7 + - - +
96D LEU* 3.2 2.6 + - - -
97D GLY* 2.7 34.3 + - - -
183D THR* 4.0 20.9 - - + -
186D PHE* 3.7 41.7 - - + -
187D GLU* 5.4 1.6 - - - +
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Residues in contact with LEU 94 (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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70D LEU* 3.8 20.0 - - + +
73D ARG* 3.5 48.0 - - + +
74D ILE* 3.2 37.0 - - + +
77D ILE* 5.3 4.9 - - + -
90D LEU 2.8 22.6 + - - +
91D ILE 3.4 2.2 - - - +
92D VAL 3.2 0.2 - - - -
93D LEU* 1.3 75.3 - - - +
95D ILE* 1.3 59.7 + - + +
97D GLY* 5.0 0.7 - - - -
98D PHE* 2.8 31.5 + - + +
101D ARG* 4.5 12.8 - - - +
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Residues in contact with ILE 95 (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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70D LEU* 4.6 25.6 - - + -
74D ILE* 5.3 1.8 - - + -
91D ILE* 3.0 27.3 + - + +
92D VAL* 3.2 6.7 + - + +
94D LEU* 1.3 80.4 - - + +
96D LEU* 1.3 65.7 + - + +
98D PHE* 3.7 2.3 - - - +
99D GLY* 3.0 20.8 + - - -
109D LEU* 5.5 5.0 - - + +
129D PHE* 6.0 5.2 - - + -
132D ILE* 3.9 32.8 - - + -
136D LEU* 5.7 1.8 - - + -
163D LEU* 5.1 5.4 - - + -
166D CYS* 4.2 29.6 - - + -
170D LEU* 4.2 23.6 - - + +
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Residues in contact with LEU 96 (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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92D VAL* 3.0 22.7 + - + +
93D LEU* 3.6 3.8 - - - +
95D ILE* 1.3 78.3 - - - +
97D GLY* 1.3 57.1 + - - +
99D GLY* 3.4 1.0 + - - -
100D GLU* 2.9 28.6 + - - +
165D PHE* 3.9 28.3 - - + -
166D CYS* 4.1 21.3 - - + +
169D MET* 3.8 23.6 - - + -
170D LEU* 4.2 9.0 - - + -
182D PRO* 3.5 32.4 - - + +
183D THR* 3.7 14.4 - - + -
186D PHE* 4.1 17.7 - - + -
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Residues in contact with GLY 97 (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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93D LEU* 2.7 21.1 + - - -
94D LEU* 3.9 1.3 - - - -
96D LEU* 1.3 70.8 - - - +
98D PHE* 1.3 65.2 + - - +
100D GLU* 3.7 2.4 - - - +
101D ARG* 3.1 41.1 + - - +
183D THR* 3.6 14.1 - - - +
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Residues in contact with PHE 98 (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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65D PHE* 4.1 20.2 - + - -
66D ILE* 3.8 30.5 - - + -
69D SER* 3.5 30.5 - - - -
70D LEU* 3.7 26.9 - - + -
73D ARG* 5.3 7.2 - - - -
94D LEU* 2.8 23.9 + - + +
95D ILE 3.7 3.1 - - - +
97D GLY* 1.3 72.8 - - - +
99D GLY* 1.3 68.3 + - - +
101D ARG* 3.4 21.1 - - - +
102D ASN* 2.9 54.6 + - + +
105D LEU* 4.1 12.3 - - + -
109D LEU* 4.9 8.1 - - + -
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Residues in contact with GLY 99 (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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95D ILE 3.0 14.3 + - - -
96D LEU 3.8 2.7 - - - -
98D PHE* 1.3 83.0 - - - +
100D GLU* 1.3 61.5 + - - +
102D ASN* 3.2 14.2 + - - -
106D THR* 2.8 30.4 + - - -
109D LEU* 5.3 4.3 - - - -
170D LEU* 4.3 10.1 - - - -
173D PHE* 3.4 8.7 - - - -
182D PRO* 4.9 0.2 - - - -
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Residues in contact with GLU 100 (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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96D LEU 2.9 15.9 + - - +
97D GLY* 3.7 6.5 - - - +
98D PHE 3.3 0.2 - - - -
99D GLY* 1.3 79.5 - - - +
101D ARG* 1.3 63.1 + - + +
102D ASN 3.3 0.9 + - - -
103D PRO* 3.7 15.1 - - - +
173D PHE* 3.8 14.2 - - + -
181D ARG* 3.4 41.4 + - + +
182D PRO* 3.5 9.8 - - + +
183D THR* 2.7 45.0 + - - -
184D ASP* 4.8 0.9 - - - +
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Residues in contact with ARG 101 (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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24D GLU* 5.5 0.9 - - - +
73D ARG* 5.2 9.9 - - - +
94D LEU* 4.5 14.3 + - - +
97D GLY* 3.1 20.0 + - - +
98D PHE* 3.4 31.8 - - - +
100D GLU* 1.3 77.4 - - + +
102D ASN* 1.3 77.1 + - - +
103D PRO* 3.6 6.9 - - - +
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Residues in contact with ASN 102 (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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24D GLU* 5.6 0.2 - - - -
65D PHE* 4.8 5.5 - - - -
98D PHE* 2.9 49.5 + - + +
99D GLY 3.2 3.4 - - - -
101D ARG* 1.3 96.4 - - - +
103D PRO* 1.3 67.1 - - - +
104D GLY 3.2 2.5 - - - -
105D LEU* 3.0 33.6 + - + +
106D THR* 2.9 20.6 + - - -
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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