Contacts of the helix formed by residues 89 - 106 (chain D) in PDB entry 6D6Q
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 VAL 89 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C GLN* 3.1 42.4 - - + +
106C SER* 5.1 0.7 - - - -
107C GLN* 3.9 20.4 - - + +
88D GLY* 1.3 78.6 - - - +
90D ALA* 1.3 69.1 + - - +
91D GLU 3.2 1.3 - - - -
92D LYS* 3.0 7.9 + - - +
93D SER* 2.9 21.0 + - - -
5F HIS 4.3 0.7 - - - +
6F ARG 4.0 27.4 - - - +
7F ARG* 4.0 16.4 - - - +
8F ILE* 4.7 9.4 - - + -
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Residues in contact with ALA 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C GLN* 3.7 30.2 - - + +
89D VAL* 1.3 78.2 - - - +
91D GLU* 1.3 65.1 + - + +
93D SER* 3.2 3.9 + - - -
94D ARG* 3.0 43.3 + - - +
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Residues in contact with GLU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LEU* 2.8 49.1 - - + +
82D PRO* 4.2 27.4 - - + +
87D PRO* 4.6 17.9 - - + -
88D GLY 4.7 5.4 - - - +
89D VAL* 3.2 0.8 - - - +
90D ALA* 1.3 80.8 - - + +
92D LYS* 1.3 56.8 + - - +
94D ARG* 3.4 28.9 + - - +
95D GLU* 2.9 32.9 + - - +
122D VAL* 5.4 0.4 - - - +
129D LEU* 5.3 3.6 - - - +
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Residues in contact with LYS 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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99C GLY 4.6 2.1 + - - -
100C GLU* 3.8 37.0 - - + +
103C GLN* 2.9 40.8 - - + +
104C VAL* 4.9 2.9 - - + -
88D GLY 4.2 9.7 + - - +
89D VAL* 3.0 13.8 + - - +
91D GLU* 1.3 76.0 - - - +
93D SER* 1.3 65.9 + - - +
95D GLU* 3.0 27.1 + - - +
96D ARG* 2.9 22.7 + - - +
6F ARG* 6.1 1.1 - - - -
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Residues in contact with SER 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C VAL* 4.1 30.5 + - - +
107C GLN* 4.7 16.4 - - - +
236C HIS* 4.8 4.7 - - - -
89D VAL 2.9 11.3 + - - -
90D ALA* 3.5 10.5 - - - -
92D LYS* 1.3 76.2 - - - +
94D ARG* 1.3 63.7 + - - +
96D ARG* 3.1 4.0 + - - +
97D LEU* 2.8 39.6 + - - +
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Residues in contact with ARG 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LEU* 4.9 8.5 - - + -
90D ALA* 3.0 28.9 + - - +
91D GLU* 3.7 29.9 + - - +
93D SER* 1.3 76.7 - - - +
95D GLU* 1.3 56.9 + - - +
97D LEU* 3.2 13.8 + - + +
98D ILE* 3.0 33.0 + - - +
129D LEU* 3.3 31.6 - - - +
130D LEU* 4.0 40.4 - - + +
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Residues in contact with GLU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C GLU* 5.1 4.0 - - - +
78D VAL* 3.2 35.4 - - + +
79D ILE* 3.2 4.1 - - - +
80D LEU* 3.0 34.7 + - + +
91D GLU 2.9 12.2 + - - +
92D LYS* 3.0 47.4 + - + +
94D ARG* 1.3 73.9 - - - +
96D ARG* 1.3 59.9 + - - +
98D ILE* 4.3 8.7 - - - -
99D ARG* 2.8 29.6 + - - +
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Residues in contact with ARG 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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100C GLU* 3.5 43.3 + - - +
101C GLU* 3.7 29.1 - - - +
104C VAL* 3.7 36.2 - - + +
236C HIS* 5.9 1.8 + - - -
238C PRO* 5.1 8.5 - - + -
92D LYS 2.9 10.6 + - - +
93D SER* 3.3 10.3 - - - +
95D GLU* 1.3 74.0 - - - +
97D LEU* 1.3 71.2 + - + +
99D ARG* 3.2 22.5 + - - +
100D ASN* 2.9 39.9 + - - +
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Residues in contact with LEU 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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104C VAL* 6.3 0.2 - - + -
236C HIS* 4.5 18.8 - - + +
237C LYS 5.3 0.4 - - - +
238C PRO* 4.5 18.8 - - + -
239C GLY 4.5 1.7 + - - -
93D SER* 2.8 42.9 + - - +
94D ARG* 3.2 13.9 + - + +
96D ARG* 1.3 81.3 - - + +
98D ILE* 1.3 63.1 + - + +
100D ASN* 3.3 1.4 + - - +
101D THR* 2.9 29.2 + - - -
130D LEU* 4.9 4.7 - - + -
194D MET* 3.5 45.8 - - + -
195D SER 5.0 1.8 - - - +
196D SER* 3.9 16.8 - - - -
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Residues in contact with ILE 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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78D VAL* 4.5 13.2 - - + -
80D LEU* 4.2 12.3 - - + -
94D ARG 3.0 21.0 + - - +
95D GLU* 3.9 6.7 - - - +
96D ARG 3.3 0.2 - - - -
97D LEU* 1.3 73.8 - - + +
99D ARG* 1.3 66.8 + - - +
101D THR* 3.3 5.8 + - - -
102D CYS* 2.9 43.3 + - - -
118D VAL* 5.6 1.1 - - + -
120D LEU* 3.8 24.0 - - + -
130D LEU* 4.4 11.4 - - + -
133D CYS* 4.4 12.1 - - + -
134D LEU* 3.6 24.9 - - + -
137D ALA* 4.6 14.1 - - + -
152D PHE* 5.6 0.4 - - + -
194D MET* 6.1 0.4 - - + -
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Residues in contact with ARG 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C GLU* 4.1 16.6 + - - -
76D LEU* 3.4 33.8 + - + +
77D GLU* 4.9 0.6 - - - +
78D VAL* 3.7 18.5 - - + +
95D GLU 2.8 19.8 + - - +
96D ARG* 3.4 38.7 - - - +
98D ILE* 1.3 76.8 - - - +
100D ASN* 1.3 81.1 + - - +
102D CYS* 3.3 2.4 + - - +
103D GLU* 2.9 42.3 + - - +
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Residues in contact with ASN 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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238C PRO* 4.1 15.3 + - - +
239C GLY* 3.8 21.4 - - - +
240C GLY 4.7 0.5 + - - -
96D ARG* 2.9 39.7 + - - +
97D LEU 4.0 1.1 - - - +
99D ARG* 1.3 96.5 + - - +
101D THR* 1.3 67.0 + - - +
103D GLU* 3.3 9.8 + - - +
104D ALA* 2.9 21.3 + - - +
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Residues in contact with THR 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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239C GLY* 4.0 8.3 - - - -
97D LEU 2.9 19.1 + - - -
98D ILE* 3.6 8.0 - - - -
100D ASN* 1.3 77.4 - - - +
102D CYS* 1.3 57.7 + - - +
104D ALA* 2.8 27.9 + - - +
105D VAL* 3.1 8.5 + - - +
134D LEU* 5.1 3.6 - - + +
152D PHE* 4.1 31.9 - - + -
184D ALA* 4.7 7.1 - - + +
193D LEU* 4.1 25.0 + - + -
194D MET* 3.8 20.4 - - - +
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Residues in contact with CYS 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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76D LEU* 3.5 26.5 - - + -
78D VAL* 5.4 0.4 - - - -
98D ILE* 2.9 33.8 + - - +
99D ARG 3.7 1.3 - - - +
101D THR* 1.3 76.4 - - - +
103D GLU* 1.3 57.3 + - - +
105D VAL* 3.1 8.4 + - - -
106D VAL* 2.6 39.1 + - + +
118D VAL* 5.4 5.2 - - - -
137D ALA* 4.9 4.0 - - - -
141D LEU* 4.1 18.8 - - + -
152D PHE* 4.0 23.6 - - - -
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Residues in contact with GLU 103 (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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73D LYS* 2.9 29.8 + - - -
74D ALA 3.4 13.6 - - - +
76D LEU* 2.9 30.6 + - + +
99D ARG* 2.9 34.6 + - - +
100D ASN* 3.6 10.3 - - - +
102D CYS* 1.3 75.8 - - - +
104D ALA* 1.3 60.9 + - - +
106D VAL* 3.6 19.0 - - - +
108D GLY* 5.9 2.4 - - - -
149D ARG* 4.9 1.2 + - - -
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Residues in contact with ALA 104 (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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240C GLY 3.7 29.6 - - - +
241C SER* 5.6 1.1 - - - -
100D ASN 2.9 11.6 + - - +
101D THR* 2.8 17.8 + - - +
103D GLU* 1.3 79.2 - - - +
105D VAL* 1.3 52.1 + - + +
149D ARG* 2.6 31.5 + - - -
193D LEU* 4.4 11.4 - - + -
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Residues in contact with VAL 105 (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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101D THR 3.1 7.5 + - - +
102D CYS* 3.5 8.1 - - - +
104D ALA* 1.3 80.5 - - + +
106D VAL* 1.3 71.9 + - + +
141D LEU* 5.4 0.9 - - + -
148D MET* 4.5 9.4 - - - -
149D ARG* 2.8 36.2 + - - +
150D ALA* 3.3 27.6 - - + +
151D LEU 4.6 1.1 - - - +
152D PHE* 3.7 32.3 - - + -
186D ASP* 4.9 6.3 - - - +
193D LEU* 3.9 28.3 - - + -
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Residues in contact with VAL 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D LEU* 4.0 16.8 - - + -
102D CYS* 2.6 35.7 + - + +
103D GLU* 3.6 22.6 - - - +
105D VAL* 1.3 78.8 - - + +
107D LEU* 1.3 73.2 + - - +
108D GLY* 3.6 4.9 + - - +
116D ILE* 4.6 9.4 - - + -
141D LEU* 5.3 6.3 - - + -
146D VAL* 4.1 23.8 - - + -
147D PRO 3.4 12.1 - - - +
148D MET* 4.1 13.2 - - + +
149D ARG* 4.6 5.1 + - - -
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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