Contacts of the strand formed by residues 51 - 62 (chain C) in PDB entry 6I53
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 THR 51 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C ARG* 3.9 8.7 - - - +
44C PRO* 3.3 46.0 - - + +
45C ASP* 4.9 5.8 - - + +
49C LYS 4.6 0.9 - - - +
50C PRO* 1.3 71.0 - - - +
52C LEU* 1.3 61.8 + - - +
53C ILE* 3.7 10.2 + - - +
82C TRP* 5.4 5.6 - - + -
83C TYR 5.4 4.5 - - - +
107C TRP* 4.1 10.4 - - + -
178C GLU 3.0 4.4 + - - +
179C ILE* 3.3 23.9 - - - +
180C VAL* 3.0 24.7 + - - +
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Residues in contact with LEU 52 (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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50C PRO 3.4 5.3 + - - +
51C THR* 1.3 71.8 - - - +
53C ILE* 1.3 60.1 + - - +
54C HIS* 3.5 26.5 + - + +
81C THR 3.7 7.8 - - - +
82C TRP* 3.9 11.4 - - - +
83C TYR* 4.6 9.8 + - + -
180C VAL* 3.4 27.1 - - + +
182C GLN* 3.3 38.6 - - + +
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Residues in contact with ILE 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C THR* 4.2 13.2 - - - +
52C LEU* 1.3 77.1 - - - +
54C HIS* 1.3 61.6 + - - +
55C THR* 3.5 4.4 + - + -
80C GLN* 4.0 27.8 - - + +
81C THR 3.4 7.9 - - - +
82C TRP* 3.9 15.7 - - + -
107C TRP* 4.5 2.0 - - + -
109C PRO* 3.7 30.5 - - + -
179C ILE* 3.7 27.8 - - + -
180C VAL 3.0 7.4 + - - +
181C TYR* 3.4 26.6 - - + -
182C GLN 3.0 24.8 + - - +
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Residues in contact with HIS 54 (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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52C LEU* 3.5 26.8 - - + +
53C ILE* 1.3 69.5 - - - +
55C THR* 1.3 64.5 + - - +
56C ASP* 4.8 0.5 - - - +
79C ALA 4.1 0.5 - - - +
80C GLN* 3.8 1.6 - - - -
81C THR* 3.0 50.7 + - - +
83C TYR* 5.1 16.5 - + - -
182C GLN* 3.2 46.4 + - - +
183C TRP 4.4 4.8 + - - -
184C LYS* 3.7 28.1 - - + +
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Residues in contact with THR 55 (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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53C ILE* 4.2 6.3 - - + +
54C HIS* 1.3 76.1 - - - +
56C ASP* 1.3 64.4 + - - +
78C PHE* 4.3 4.0 - - + -
79C ALA 3.3 7.9 - - - -
80C GLN* 4.3 9.4 - - + +
169C PHE* 3.7 25.5 - - + -
181C TYR* 3.6 34.3 - - + -
182C GLN 3.1 10.9 + - - +
183C TRP* 3.3 28.4 - - - -
184C LYS* 3.6 21.7 + - - +
187C SER 4.9 0.2 - - - +
223C MET* 4.6 1.6 - - - +
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Residues in contact with ASP 56 (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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54C HIS 4.8 0.7 - - - +
55C THR* 1.3 78.8 - - - +
57C MET* 1.3 66.7 + - - +
77C PHE 3.8 0.9 - - - +
78C PHE* 3.6 3.0 - - - -
79C ALA* 2.7 54.2 + - + +
81C THR* 6.5 0.4 - - + -
183C TRP* 4.6 1.8 - - - -
184C LYS* 4.1 19.2 - - + +
186C SER* 2.9 24.0 + - - +
187C SER 2.9 20.4 - - - +
189C GLU* 5.5 2.1 - - - +
206D SER* 5.2 7.4 + - - -
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Residues in contact with MET 57 (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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56C ASP* 1.3 80.1 + - - +
58C TYR* 1.3 61.8 + - - +
59C VAL* 4.0 12.7 + - + -
76C ILE* 3.8 40.4 - - + -
77C PHE 3.5 3.4 - - - +
78C PHE* 3.9 21.8 - - + +
113C PHE* 4.4 1.1 - - + -
167C LEU* 4.0 21.8 - - + -
169C PHE* 3.9 24.0 - - + -
183C TRP* 4.5 3.8 - - + -
187C SER 2.9 13.4 + - - +
188C VAL* 3.4 11.8 - - + -
189C GLU* 2.9 25.8 + - - +
225C VAL* 4.5 15.7 - - + -
227C PHE* 4.9 2.2 - - - -
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Residues in contact with TYR 58 (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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57C MET* 1.3 72.5 - - - +
59C VAL* 1.3 69.6 + - - +
60C ASN* 3.1 12.0 + - - -
76C ILE* 3.3 2.0 - - - -
77C PHE* 2.8 71.1 + + + +
189C GLU* 3.5 49.4 - - + +
190C VAL 4.4 8.5 - - - -
191C GLY* 3.9 18.3 - - - -
206D SER* 5.7 5.8 - - - +
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Residues in contact with VAL 59 (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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57C MET* 4.4 3.6 - - - -
58C TYR* 1.3 72.3 - - - +
60C ASN* 1.3 64.7 + - - +
61C SER 3.9 20.2 - - - +
62C ILE* 3.9 20.9 - - + -
74C ILE* 4.2 6.3 - - + -
75C ASP 3.8 3.4 - - - -
76C ILE* 3.9 13.5 - - + -
188C VAL* 4.0 17.7 - - + -
189C GLU 2.9 13.0 + - - +
190C VAL* 4.9 3.8 - - + -
191C GLY* 3.6 20.4 + - - -
196C TRP* 4.1 15.7 - - + -
227C PHE* 3.7 28.5 - - + -
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Residues in contact with ASN 60 (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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58C TYR* 3.1 13.9 + - - -
59C VAL* 1.3 74.4 - - - +
61C SER* 1.3 61.1 + - - +
75C ASP* 2.7 28.3 + - - +
77C PHE* 3.8 30.6 - - + -
144C ARG* 3.5 25.9 - - - +
191C GLY* 5.2 3.3 - - - -
192C ASP* 5.1 1.9 - - - +
195C SER* 5.1 2.1 + - - -
196C TRP* 3.2 14.8 + - - -
102D HIS 3.7 10.5 + - - -
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Residues in contact with SER 61 (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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59C VAL* 3.5 2.5 - - - +
60C ASN* 1.3 82.1 - - - +
62C ILE* 1.3 66.7 + - - +
63C GLY* 4.9 1.7 + - - -
74C ILE* 3.5 6.1 - - - +
75C ASP* 2.9 42.1 + - - +
195C SER* 5.0 1.6 - - - -
196C TRP* 3.5 24.5 - - - +
197C ARG* 5.2 3.5 - - - -
138D GLU* 4.4 19.7 + - - -
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Residues in contact with ILE 62 (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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59C VAL* 3.9 11.0 - - + -
61C SER* 1.3 77.9 - - - +
63C GLY* 1.3 73.0 + - - +
65C VAL* 5.0 2.5 - - + -
72C TYR* 4.3 17.5 - - + -
73C THR 3.4 9.2 - - - +
74C ILE* 4.2 9.2 - - + +
196C TRP* 3.6 38.3 - - + +
197C ARG 3.3 22.7 + - - -
198C LEU* 3.9 19.6 - - + +
203C PHE* 4.4 5.4 - - + -
227C PHE* 3.8 36.6 - - + -
229C LEU* 5.2 6.1 - - + -
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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
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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