Contacts of the strand formed by residues 36 - 51 (chain C) in PDB entry 6D6U
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 36 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ARG* 4.3 5.5 - - - +
29C PRO* 4.3 25.1 - - + +
30C ASP* 5.3 6.5 - - + +
35C PRO* 1.3 74.4 - - - +
37C ALA* 1.3 69.9 + - - +
38C VAL* 3.5 3.6 + - + -
67C TRP* 4.4 10.8 - - + -
68C ARG* 3.7 24.7 - - + +
92C TRP* 4.2 19.5 - - + -
163C ASP 3.2 13.9 + - - +
164C ILE* 3.9 13.0 - - + +
165C GLU* 3.1 25.7 + - - +
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Residues in contact with ALA 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PRO 4.1 1.2 + - - -
36C VAL* 1.3 73.0 - - - +
38C VAL* 1.3 62.4 + - - +
39C GLY 3.9 1.5 + - - -
66C ALA 4.0 0.5 - - - +
67C TRP* 3.4 21.9 - - - +
68C ARG* 4.1 5.0 + - + +
165C GLU* 4.0 10.1 - - + -
167C TYR* 3.8 27.0 + - + +
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Residues in contact with VAL 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C VAL* 4.4 8.3 - - + -
37C ALA* 1.3 74.1 - - - +
39C GLY* 1.3 59.8 + - - +
40C MET* 3.9 6.8 + - + -
65C GLN* 4.2 18.2 - - + +
66C ALA 4.1 3.4 - - - +
67C TRP* 3.8 19.3 - - + -
92C TRP* 4.9 0.9 - - + -
94C PRO* 4.0 24.2 - - + -
164C ILE* 3.8 26.2 - - + -
165C GLU 2.9 23.6 + - - +
166C PHE* 3.4 32.8 - - + -
167C TYR* 3.6 4.4 + - - -
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Residues in contact with GLY 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ALA 3.9 1.4 + - - -
38C VAL* 1.3 73.8 - - - +
40C MET* 1.3 62.4 + - - -
41C ASN* 4.1 1.0 + - - +
65C GLN* 3.3 1.6 - - - -
66C ALA* 3.0 38.9 + - - +
167C TYR* 3.4 28.7 - - - -
169C ARG* 4.9 13.9 + - - +
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Residues in contact with MET 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C VAL* 3.9 6.4 + - + +
39C GLY* 1.3 73.9 - - - -
41C ASN* 1.3 61.0 + - - +
63C PHE* 3.4 31.4 - - + -
64C GLN 3.5 4.3 - - - +
65C GLN* 3.6 26.9 - - + +
96C THR* 4.4 6.3 - - - -
154C ILE* 3.6 23.6 - - + -
166C PHE* 3.4 41.3 - - + -
167C TYR 3.4 5.9 + - - -
168C TRP* 3.6 21.4 - - + -
169C ARG* 3.5 19.4 + - - -
208C LEU* 3.5 24.0 - - + -
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Residues in contact with ASN 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B SER* 4.7 14.3 + - - -
39C GLY 4.1 0.6 + - - +
40C MET* 1.3 75.0 - - - +
42C ILE* 1.3 71.3 + - - +
43C ASP* 5.7 0.6 - - - +
62C TYR 3.9 0.7 - - - +
63C PHE 3.8 0.2 - - - -
64C GLN* 2.6 56.8 + - + +
168C TRP* 4.9 0.2 - - - -
169C ARG* 3.6 41.6 + - + +
173C ASN 3.8 10.9 + - - +
174C ALA* 2.8 28.5 - - - +
176C THR* 5.8 0.9 - - - +
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Residues in contact with ILE 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C MET 5.5 0.2 - - - -
41C ASN* 1.3 83.9 + - - +
43C ASP* 1.3 64.8 + - - +
44C ILE* 4.0 20.9 - - + -
61C MET* 3.8 27.8 - - + -
62C TYR 3.8 2.9 - - - +
63C PHE* 3.7 21.8 - - + -
152C LEU* 5.2 1.6 - - + -
154C ILE* 3.7 22.4 - - + -
168C TRP* 3.6 32.3 - - + -
174C ALA 2.9 22.3 + - - +
175C VAL* 3.3 18.6 - - + -
176C THR* 3.6 2.8 + - - +
210C LEU* 4.8 11.9 - - + -
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Residues in contact with ASP 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B SER* 5.2 5.9 - - - -
206B SER* 4.2 19.0 + - - +
41C ASN* 5.7 0.7 - - - +
42C ILE* 1.3 73.7 - - - +
44C ILE* 1.3 70.9 + - - +
45C ALA 3.8 0.2 + - - -
61C MET* 3.3 1.5 - - - -
62C TYR* 2.5 65.4 + - + +
64C GLN* 6.0 2.9 - - - +
176C THR* 2.8 30.6 + - - +
177C GLY* 4.2 1.7 + - - -
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Residues in contact with ILE 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ILE* 4.0 14.8 + - + -
43C ASP* 1.3 85.3 + - - +
45C ALA* 1.3 64.1 + - - +
46C SER* 4.0 15.0 - - - +
47C ILE* 4.6 17.0 - - + -
59C LEU* 5.3 9.6 - - + -
60C THR 4.3 4.0 - - - +
61C MET* 4.0 11.7 - - + -
175C VAL* 3.9 22.2 - - + -
176C THR 3.3 14.0 + - - +
177C GLY* 4.0 15.0 - - - +
178C VAL* 4.0 14.8 - - + -
181C ILE* 5.6 5.8 - - + -
210C LEU* 4.0 20.2 - - + -
212C PHE* 5.1 10.5 - - + -
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Residues in contact with ALA 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B HIS 5.8 3.4 - - - +
43C ASP 3.8 1.0 + - - -
44C ILE* 1.3 76.7 - - - +
46C SER* 1.3 65.5 + - - +
60C THR* 2.8 26.7 + - + +
61C MET* 4.9 0.4 - - - +
62C TYR* 4.6 25.6 - - + +
129C ARG* 6.2 0.7 - - - +
177C GLY 5.6 0.9 - - - +
181C ILE* 4.3 7.1 - - - +
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Residues in contact with SER 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLU* 3.9 18.7 + - - -
44C ILE* 3.9 2.9 - - - +
45C ALA* 1.3 82.8 - - - +
47C ILE* 1.3 65.4 + - - +
48C ASP* 3.4 18.7 + - - -
59C LEU* 3.4 1.9 - - - +
60C THR* 2.9 37.9 + - - +
181C ILE* 3.5 12.6 - - - -
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Residues in contact with ILE 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ILE* 4.6 13.5 - - + -
46C SER* 1.3 76.8 - - - +
48C ASP* 1.3 65.0 + - - +
49C MET 4.7 1.8 - - - +
50C VAL* 4.7 13.2 - - + -
57C TYR* 4.4 15.0 - - + -
58C THR 3.3 11.7 - - - +
59C LEU* 4.0 15.7 - - + -
181C ILE* 3.3 23.6 - - + +
182C GLU 5.0 1.2 - - - +
183C LEU* 3.2 33.1 - - + +
188C ILE* 4.9 8.7 - - + -
212C PHE* 3.7 35.4 - - + -
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Residues in contact with ASP 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LYS* 4.1 28.4 - - - +
138B GLU* 3.9 14.2 - - - +
46C SER* 3.4 20.0 + - - -
47C ILE* 1.3 77.1 - - - +
49C MET* 1.3 65.9 + - + +
58C THR* 2.8 35.8 + - + +
60C THR* 4.3 9.1 + - - -
131C THR* 5.3 0.9 - - - +
183C LEU* 4.8 3.7 - - - +
184C PRO* 4.8 10.7 - - - +
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Residues in contact with MET 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ILE* 3.7 1.8 - - - +
48C ASP* 1.3 89.0 - - + +
50C VAL* 1.3 65.5 + - - +
51C SER* 4.2 23.1 - - - +
56C ASP 4.1 1.5 - - - +
57C TYR* 3.3 6.1 - - - +
58C THR* 3.3 32.2 + - - +
183C LEU* 5.8 1.1 - - - -
184C PRO* 6.2 2.0 - - - -
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Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ILE* 4.7 11.4 - - + -
49C MET* 1.3 80.4 - - - +
51C SER* 1.3 62.0 + - - +
52C GLU* 4.1 10.3 + - - +
56C ASP 3.9 2.9 - - - -
57C TYR* 3.8 14.8 - - + -
138C MET* 3.5 29.2 - - + -
148C GLN* 4.7 0.7 - - - +
183C LEU* 5.0 7.8 - - + +
185C GLN* 5.6 1.7 - - - +
186C PHE* 3.5 41.8 - - + -
214C LEU* 4.6 14.1 - - + -
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Residues in contact with SER 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C MET* 4.2 21.6 - - - +
50C VAL* 1.3 73.3 - - - +
52C GLU* 1.3 61.0 + - - +
53C VAL* 3.6 16.3 + - - +
54C ASN* 3.8 14.1 + - - -
55C MET* 2.9 27.4 + - - -
56C ASP* 3.3 24.7 + - - -
138C MET* 4.3 3.6 - - - +
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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
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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