Contacts of the helix formed by residues 90 - 107 (chain D) in PDB entry 2WZJ
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 ASN 90 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C LYS* 4.4 12.1 + - - +
88D GLN 5.1 2.0 + - - -
89D LEU* 1.3 79.8 - - - +
91D SER* 1.3 56.1 + - - +
92D SER* 3.5 20.3 + - - +
93D SER* 2.5 48.5 + - - -
94D LEU* 2.9 8.7 + - - -
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Residues in contact with SER 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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170C PHE* 5.6 4.5 - - - -
227C ASP* 5.1 1.3 - - - -
228C GLY* 4.1 17.7 - - - -
229C PRO* 3.9 19.8 - - - +
230C GLU* 5.1 2.8 + - - -
89D LEU 4.4 0.4 + - - -
90D ASN* 1.3 71.3 - - - +
92D SER* 1.3 65.3 + - - +
94D LEU* 3.4 14.9 + - - +
95D GLN* 3.2 30.9 + - - +
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Residues in contact with SER 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C LYS* 4.5 9.0 - - - -
227C ASP* 3.7 34.4 + - - +
90D ASN* 2.8 17.1 + - - -
91D SER* 1.3 78.5 - - - +
93D SER* 1.3 63.8 + - - -
95D GLN* 3.3 16.0 + - - +
96D LYS* 3.4 10.6 + - - +
99D ARG* 5.1 2.1 + - - -
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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
----------------------------------------------------------
89D LEU* 4.0 24.3 - - - +
90D ASN* 2.5 35.6 + - - -
92D SER* 1.3 74.9 + - - +
94D LEU* 1.3 56.4 + - - -
96D LYS* 2.7 33.0 + - - +
97D LEU* 2.9 11.4 + - - +
202D PHE* 4.6 15.0 + - - +
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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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170C PHE* 3.8 32.5 - - + -
86D LYS* 4.2 30.3 - - + +
89D LEU* 3.6 41.7 - - + +
90D ASN 2.9 9.4 + - - +
91D SER* 3.8 15.9 - - - +
93D SER* 1.3 76.5 - - - +
95D GLN* 1.3 61.2 + - - +
97D LEU* 3.4 9.7 + - + +
98D PHE* 3.2 33.6 + - + -
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Residues in contact with GLN 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C PHE* 3.9 35.9 - - + +
171C ILE* 5.9 0.2 - - - -
172C VAL* 3.5 17.9 + - - +
174C ARG* 3.4 21.6 + - - +
227C ASP* 2.9 31.1 + - - +
228C GLY* 4.5 2.8 - - - -
229C PRO* 4.9 1.2 - - - +
91D SER* 3.2 21.9 + - - +
92D SER* 3.6 9.2 - - - +
93D SER 3.1 0.8 - - - -
94D LEU* 1.3 74.6 - - - +
96D LYS* 1.3 61.3 + - - +
98D PHE* 4.5 0.4 - - - +
99D ARG* 2.9 44.4 + - - +
102D ARG* 4.6 2.6 + - - -
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Residues in contact with LYS 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 SER 3.4 6.9 + - - +
93D SER* 2.7 18.6 + - - +
95D GLN* 1.3 72.5 - - - +
97D LEU* 1.3 60.3 + - - +
99D ARG* 3.3 27.7 - - - +
100D GLU* 2.5 63.0 + - - +
200D PHE* 4.3 21.3 - - + -
202D PHE* 4.6 13.7 - - + -
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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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84D ILE* 3.9 23.6 - - + -
86D LYS* 4.7 4.7 - - + -
89D LEU* 4.0 19.3 - - + -
93D SER 2.9 8.7 + - - +
94D LEU* 3.4 19.5 - - + +
96D LYS* 1.3 76.8 - - - +
98D PHE* 1.3 67.1 + - + +
100D GLU* 3.3 5.5 + - - +
101D VAL* 2.9 36.4 + - + +
125D LEU* 3.8 26.0 - - + -
196D PHE* 3.7 33.2 - - + -
202D PHE* 4.1 13.2 - - + -
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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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169C LYS* 4.4 4.5 - - - +
170C PHE* 3.4 44.2 - + + -
86D LYS* 4.7 8.3 - - + -
94D LEU* 3.2 25.9 + - + +
95D GLN 4.5 0.4 - - - +
97D LEU* 1.3 89.3 - - + +
99D ARG* 1.3 66.1 + - - +
101D VAL* 3.9 15.8 - - + +
102D ARG* 3.0 41.5 + - - +
118D VAL* 5.6 3.4 - - + -
120D GLU* 3.3 35.0 - - - -
125D LEU* 4.4 22.4 - - + -
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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
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99C ARG* 3.8 33.9 - - + +
103C ILE* 6.3 2.7 - - - -
92D SER 5.1 2.2 + - - -
95D GLN* 2.9 41.4 + - - +
96D LYS* 3.3 39.1 + - - +
98D PHE* 1.3 75.0 - - - +
100D GLU* 1.3 67.7 + - + +
102D ARG* 3.1 29.1 + - - +
103D ILE* 3.0 31.4 + - + +
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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 LYS* 2.5 58.2 + - - +
97D LEU* 3.7 4.0 - - - +
99D ARG* 1.3 81.3 + - + +
101D VAL* 1.3 57.0 + - - +
103D ILE* 3.0 19.1 + - + +
104D MET* 2.9 28.5 + - - +
195D GLY* 3.3 35.0 - - - +
196D PHE* 3.6 22.9 - - + +
197D SER* 4.4 2.6 + - - -
200D PHE* 5.1 3.8 - - - -
202D PHE* 5.0 3.3 - - - -
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Residues in contact with VAL 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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97D LEU* 2.9 28.4 + - + +
98D PHE* 3.9 17.9 - - + +
99D ARG 3.3 0.2 - - - -
100D GLU* 1.3 76.9 - - - +
102D ARG* 1.3 58.6 + - + +
104D MET* 3.2 13.4 + - + +
105D LYS* 3.0 48.2 + - + +
115D LEU* 4.7 2.5 - - + -
118D VAL* 4.3 17.5 - - + -
125D LEU* 4.6 4.5 - - + -
127D LEU* 3.7 37.0 - - + -
196D PHE* 5.0 0.7 - - + -
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Residues in contact with ARG 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ARG* 6.5 0.9 - - - -
103C ILE* 4.2 23.6 - - - +
106C VAL* 4.3 28.7 - - + -
169C LYS* 3.4 29.5 + - - +
170C PHE 3.7 7.3 + - - -
171C ILE* 3.6 20.1 - - - +
95D GLN 4.6 1.4 + - - -
98D PHE* 3.0 20.3 + - - +
99D ARG* 3.1 44.5 + - - +
101D VAL* 1.3 73.6 - - + +
103D ILE* 1.3 67.5 + - + +
105D LYS* 3.4 24.0 + - + +
106D VAL* 3.4 13.9 + - - +
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Residues in contact with ILE 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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99C ARG* 6.1 3.8 - - + -
102C ARG* 4.8 21.3 - - - +
99D ARG* 3.0 22.3 + - + +
100D GLU* 3.0 22.6 + - + +
102D ARG* 1.3 76.1 - - + +
104D MET* 1.3 57.9 + - - +
106D VAL* 2.9 29.9 + - + +
107D LEU* 3.2 20.7 + - + +
171D ILE* 4.0 30.3 - - + -
194D PHE 4.5 5.8 - - - +
195D GLY* 4.4 12.6 - - - -
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Residues in contact with MET 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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100D GLU 2.9 7.6 + - - +
101D VAL* 3.2 21.1 + - + +
103D ILE* 1.3 78.7 - - - +
105D LYS* 1.3 61.8 + - - +
106D VAL 3.1 1.2 + - - -
107D LEU* 3.7 18.8 + - + +
113D VAL* 5.7 9.2 - - + +
114D LYS* 5.8 1.0 - - - +
115D LEU* 4.2 28.8 + - + +
127D LEU* 3.8 21.8 - - + -
129D MET* 3.7 26.5 - - + +
195D GLY* 4.3 7.9 - - - +
196D PHE* 3.2 47.1 - - + +
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Residues in contact with LYS 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 VAL* 3.0 35.4 + - - +
102D ARG* 3.7 16.6 - - + +
103D ILE 3.3 0.4 - - - -
104D MET* 1.3 75.8 - - - +
106D VAL* 1.3 59.7 + - + +
107D LEU 4.8 2.5 - - - +
108D ASN* 6.1 0.3 - - - +
114D LYS* 5.4 5.5 + - - -
115D LEU* 3.9 16.8 - - + +
118D VAL* 4.5 14.7 - - - +
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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
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102C ARG* 4.7 22.2 - - + +
102D ARG 3.4 10.1 + - - +
103D ILE* 2.9 25.3 + - + +
105D LYS* 1.3 78.7 - - + +
107D LEU* 1.3 75.2 + - + +
108D ASN* 3.4 6.2 + - - +
165D TYR* 3.8 6.8 + - - -
169D LYS* 4.8 14.4 + - + +
171D ILE* 5.1 2.2 - - + -
318D GLU* 4.8 4.7 - - - +
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Residues in contact with LEU 107 (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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103D ILE* 3.2 22.3 + - + +
104D MET* 3.7 14.9 + - + +
105D LYS 4.8 1.8 - - - +
106D VAL* 1.3 81.4 + - + +
108D ASN* 1.3 58.9 + - - +
109D HIS 3.8 1.8 + - - -
112D ILE* 4.2 17.6 - - + +
113D VAL 6.1 0.2 - - - +
114D LYS* 4.6 15.4 + - - +
165D TYR* 4.0 21.5 - - + -
166D CYS* 4.0 17.9 - - + -
169D LYS* 4.4 8.1 - - + -
171D ILE* 4.0 25.6 - - + -
194D PHE* 3.6 32.3 - - + -
195D GLY 5.1 0.9 - - - +
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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