Contacts of the helix formed by residues 93 - 111 (chain M) in PDB entry 6KW5
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 ILE 93 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H SER 5.3 1.8 - - - +
85H PHE 4.3 16.2 - - - +
87H SER* 3.9 24.9 - - - +
88H TRP* 4.5 20.2 - - + +
88M ALA 4.7 0.3 - - - +
91M SER* 3.7 6.0 + - - +
92M GLY* 1.3 79.8 - - - +
94M PRO* 1.3 74.4 - - + +
95M GLU* 4.3 5.4 - - + +
96M GLU* 3.3 24.7 + - + +
97M ILE* 3.0 23.6 + - - +
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Residues in contact with PRO 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92M GLY 3.3 9.2 - - - +
93M ILE* 1.3 90.4 - - + +
95M GLU* 1.3 59.5 + - + +
97M ILE* 3.2 14.5 + - + +
98M LYS* 2.9 33.3 + - - +
153M ASP* 4.4 9.2 - - - +
157M MET* 3.4 13.9 - - + +
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Residues in contact with GLU 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277J ARG* 3.5 35.6 + - - +
93M ILE* 3.4 5.6 - - + +
94M PRO* 1.3 82.9 - - + +
96M GLU* 1.3 70.3 + - - +
98M LYS* 3.2 16.1 + - + +
99M TRP* 3.0 31.0 + - - +
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Residues in contact with GLU 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D PRO* 4.1 16.9 - - - +
84H SER* 3.5 25.5 + - - +
85H PHE* 4.4 16.2 - - + -
84M ARG* 4.8 6.4 - - - -
88M ALA* 3.7 22.9 - - + +
91M SER* 5.2 0.4 - - - +
93M ILE* 3.3 25.2 + - + +
94M PRO 3.3 0.6 - - - -
95M GLU* 1.3 85.9 + - - +
97M ILE* 1.3 60.7 + - - +
99M TRP* 3.4 29.4 + - - +
100M SER* 2.9 28.6 + - - -
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Residues in contact with ILE 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88M ALA 3.6 17.0 - - - +
89M LEU* 3.8 15.9 - - + +
91M SER 4.1 17.0 - - - +
92M GLY* 4.2 6.5 - - - +
93M ILE 3.0 24.6 + - - +
94M PRO* 3.4 10.8 - - + +
96M GLU* 1.3 74.4 - - - +
98M LYS* 1.3 58.9 + - - +
100M SER* 3.3 1.1 + - - -
101M LEU* 2.9 35.0 + - + +
130M PHE* 3.7 34.3 - - + -
157M MET* 3.7 23.8 - - + -
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Residues in contact with LYS 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277J ARG* 4.1 28.9 - - - +
278J ASP* 3.5 25.5 + - - +
94M PRO* 2.9 26.2 + - - +
95M GLU* 3.3 15.5 - - + +
97M ILE* 1.3 76.7 - - - +
99M TRP* 1.3 63.4 + - - +
101M LEU* 3.4 6.4 + - - +
102M LYS* 3.0 24.8 + - - +
153M ASP* 2.4 40.9 + - - +
157M MET* 3.9 11.4 - - + -
160M ASN* 5.7 0.3 + - - -
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Residues in contact with TRP 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D PRO* 3.9 30.6 - - + +
81M ASP* 4.8 9.4 - - - -
84M ARG* 3.6 35.4 - - + -
85M MET* 4.1 31.0 - - + -
88M ALA* 4.7 0.7 - - + -
95M GLU* 3.0 20.9 + - - +
96M GLU* 3.6 31.6 - - - +
98M LYS* 1.3 74.7 - - - +
100M SER* 1.3 75.9 + - - +
102M LYS* 3.3 19.8 + - - +
103M LYS* 3.0 47.8 + - + +
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Residues in contact with SER 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85M MET* 2.8 31.5 + - - +
88M ALA* 3.7 17.3 - - - -
89M LEU* 3.3 18.6 - - - +
96M GLU 2.9 17.0 + - - -
97M ILE 3.3 3.8 + - - -
99M TRP* 1.3 85.4 - - - +
101M LEU* 1.3 59.8 + - - +
103M LYS* 3.4 3.3 + - - +
104M TYR* 2.9 30.4 + - - +
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Residues in contact with LEU 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89M LEU* 3.8 26.0 - - + -
97M ILE* 2.9 27.4 + - + +
98M LYS* 4.0 4.3 - - - +
100M SER* 1.3 72.4 - - - +
102M LYS* 1.3 60.5 + - - +
104M TYR* 3.8 3.1 - - + -
105M LEU* 2.9 30.5 + - - +
127M PHE* 4.5 8.7 - - + -
130M PHE* 5.0 7.0 - - + -
157M MET* 3.9 46.0 - - + +
160M ASN* 4.1 17.7 + - + +
161M ALA* 4.7 8.3 - - + -
164M ILE* 3.8 22.4 - - + +
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Residues in contact with LYS 102 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271J HIS* 4.7 26.4 + - + +
286J GLN* 6.0 1.3 - - - +
166K HIS* 5.6 7.5 - - - -
98M LYS 3.0 18.5 + - - +
99M TRP* 3.7 20.5 - - - +
101M LEU* 1.3 77.4 - - - +
103M LYS* 1.3 86.5 + - - +
105M LEU* 3.3 8.6 + - + +
106M THR* 3.0 36.8 + - - +
160M ASN* 4.6 6.4 - - - +
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Residues in contact with LYS 103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164K ILE* 6.1 2.4 - - - +
166K HIS* 5.5 9.1 + - - +
85M MET* 3.6 30.3 - - + -
99M TRP* 3.0 49.1 + - + +
100M SER 4.0 2.0 - - - +
102M LYS* 1.3 106.1 - - - +
104M TYR* 1.3 59.0 + - - +
106M THR* 3.3 17.5 + - - +
107M TYR* 2.9 43.4 + - + -
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Residues in contact with TYR 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82M LEU* 4.4 9.5 + - + +
85M MET* 3.8 33.4 - - + +
86M GLU* 3.8 25.5 + - - +
89M LEU* 3.6 26.5 - - + -
100M SER 2.9 18.4 + - - +
101M LEU* 3.8 4.7 - - + +
103M LYS* 1.3 75.4 - - - +
105M LEU* 1.3 58.6 + - - +
107M TYR* 3.5 0.4 + - + -
108M SER* 2.9 30.8 + - - -
115M ILE* 3.7 32.0 - - + +
120M LEU* 5.4 1.9 - - - +
123M LEU* 3.8 19.8 - - + +
126M LEU* 4.8 4.5 - - + +
127M PHE* 3.5 30.1 - + + -
164M ILE* 3.8 14.4 - - + +
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Residues in contact with LEU 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286J GLN 4.6 1.1 - - - +
287J ARG* 4.5 10.1 - - - -
290J GLN* 3.7 30.7 - - + -
101M LEU 2.9 18.7 + - - +
102M LYS* 3.6 7.2 - - + +
103M LYS 3.2 0.2 - - - -
104M TYR* 1.3 77.2 - - - +
106M THR* 1.3 57.7 + - - +
108M SER* 2.7 25.6 + - - +
109M ASN* 3.0 16.1 + - - +
160M ASN* 3.3 23.8 - - - +
163M LEU* 3.7 27.8 - - + -
164M ILE* 3.8 17.6 - - + +
167M ASN* 3.8 10.3 - - - +
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Residues in contact with THR 106 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290J GLN* 3.7 18.3 + - - +
164K ILE* 3.8 32.3 - - + -
166K HIS* 6.3 1.6 - - + +
102M LYS* 3.0 28.2 + - - +
103M LYS* 3.8 22.1 + - - +
105M LEU* 1.3 75.9 - - - +
107M TYR* 1.3 59.2 + - + +
109M ASN* 3.4 0.7 + - - +
110M LYS* 2.9 36.5 + - + +
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Residues in contact with TYR 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C ASP* 2.4 38.3 + - - +
199C MET* 3.7 21.1 - - + -
162K PRO* 4.7 8.4 + - + -
164K ILE* 3.6 31.3 - - + +
85M MET* 3.6 28.0 - - + -
103M LYS* 2.9 36.2 + - + +
104M TYR* 5.4 0.4 - - + -
106M THR* 1.3 78.2 - - - +
108M SER* 1.3 58.5 + - - +
110M LYS 4.0 0.7 - - - +
111M ALA* 2.9 41.9 + - + +
112M PRO* 3.9 0.3 - - - +
114M MET* 4.8 14.4 - - + -
115M ILE* 3.6 22.6 - - + +
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Residues in contact with SER 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292J ARG* 3.9 6.6 + - - -
104M TYR 2.9 17.1 + - - -
105M LEU* 2.7 33.6 + - - +
107M TYR* 1.3 74.3 - - - +
109M ASN* 1.3 64.5 + - - +
112M PRO* 3.3 28.0 - - - +
115M ILE* 4.0 5.8 - - - +
164M ILE* 4.3 12.5 - - - +
167M ASN* 4.0 17.7 + - - +
168M LEU* 4.3 17.3 - - - -
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Residues in contact with ASN 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C PHE* 4.1 7.6 - - - -
219C LYS* 4.5 6.6 + - - -
289J VAL 4.2 3.4 + - - -
290J GLN* 3.3 58.4 + - - +
291J ILE 4.6 1.6 + - - +
292J ARG* 3.6 35.8 - - - +
105M LEU 3.0 16.3 + - - +
106M THR 3.9 0.9 - - - +
108M SER* 1.3 80.7 + - - +
110M LYS* 1.3 76.0 + - + +
112M PRO* 4.4 0.3 - - - +
167M ASN* 5.2 0.7 - - - +
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Residues in contact with LYS 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C PHE* 3.3 21.7 - - - -
219C LYS* 4.6 14.8 + - - +
290J GLN* 4.9 9.3 + - - +
164K ILE* 3.8 33.9 - - + +
165K PHE* 2.9 42.8 + - + +
181K GLU* 5.4 7.4 - - - +
106M THR* 2.9 25.8 + - + +
109M ASN* 1.3 97.6 - - + +
111M ALA* 1.3 61.0 + - - +
112M PRO* 4.1 1.6 - - - -
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Residues in contact with ALA 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C PHE* 5.0 0.7 - - - -
162K PRO* 4.0 27.1 - - + -
164K ILE* 5.7 1.1 - - + -
107M TYR* 2.9 21.8 + - + +
110M LYS* 1.3 81.3 - - + +
112M PRO* 1.3 70.1 - - - +
113M TYR* 3.2 26.3 + - + +
114M MET* 3.4 18.1 + - + +
115M ILE 4.3 0.7 + - - -
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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
------------------------------------------------------------
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