Contacts of the strand formed by residues 43 - 55 (chain C) in PDB entry 5IYB
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 PRO 43 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C GLU 3.3 8.9 - - - +
42C VAL* 1.3 101.2 - - + +
44C ILE* 1.3 63.4 + - - +
79C VAL* 4.0 21.9 - - + +
84C TYR* 4.2 13.5 - - + +
167C LYS* 3.9 24.0 - - + +
168C GLY 3.8 8.1 - - - +
169C PHE* 4.4 4.5 - - + -
239C LEU* 5.2 4.9 - - - +
247C SER* 5.0 15.7 - - - +
251C GLY* 6.3 2.2 - - - -
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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
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42C VAL 4.6 1.1 - - - +
43C PRO* 1.3 77.1 - - - +
45C ILE* 1.3 77.1 + - - +
73C LEU 5.7 0.2 - - - +
75C SER* 4.1 13.5 - - - +
79C VAL* 4.6 8.7 - - - -
167C LYS* 3.2 7.8 - - - +
168C GLY 3.2 26.2 + - - +
175C LYS 4.7 2.7 - - - +
176C TRP* 3.4 44.7 - - + +
177C ASN 3.9 15.5 - - - +
178C PRO* 4.0 14.8 - - + -
238C SER* 3.4 35.4 - - - +
239C LEU* 5.2 5.4 - - + -
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Residues in contact with ILE 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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44C ILE* 1.3 91.7 - - - +
46C ALA* 1.3 65.6 + - - +
73C LEU* 3.4 26.1 + - + +
75C SER* 3.4 18.9 + - - +
77C ASP 5.7 1.1 - - - +
79C VAL* 4.1 18.8 - - + -
82C LEU* 3.5 31.4 - - + -
99C VAL* 4.5 7.9 - - + -
128C ILE* 4.2 22.7 - - + -
165C ALA* 3.6 24.9 - - + -
166C LYS 3.6 10.1 - - - +
167C LYS* 4.5 2.2 - - - +
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Residues in contact with ALA 46 (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* 5.0 0.7 - - + -
45C ILE* 1.3 77.7 - - - +
47C ILE* 1.3 68.5 + - - +
48C ASP* 3.3 2.4 + - - +
69C GLY 4.3 10.5 - - - +
71C ILE 4.9 3.8 - - - +
72C PRO* 6.3 0.4 - - + -
73C LEU* 3.8 8.3 - - - +
165C ALA* 3.6 6.1 - - - -
166C LYS 3.1 26.6 + - - +
175C LYS* 4.3 17.7 - - + +
176C TRP* 3.5 25.1 + - + +
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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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46C ALA* 1.3 74.0 - - - +
48C ASP* 1.3 62.0 + - - +
49C TRP 4.1 2.0 - - - +
50C VAL* 3.7 17.0 - - + -
68C LEU* 3.5 44.6 - - + +
69C GLY* 3.9 7.0 + - - -
71C ILE* 3.7 22.8 + - + -
73C LEU* 4.1 6.7 - - + +
101C PHE* 4.5 18.8 - - + -
120C LEU* 4.2 8.5 - - + -
163C ALA* 3.7 29.4 - - + -
164C TYR 4.5 1.3 - - - +
165C ALA* 3.9 7.4 - - + +
175C LYS* 3.3 18.0 + - - +
57L ALA* 3.8 6.3 - - + +
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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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46C ALA 3.3 3.5 + - - +
47C ILE* 1.3 75.9 - - - +
49C TRP* 1.3 62.4 + - - +
164C TYR 3.1 8.7 + - - +
166C LYS* 3.1 39.5 + - + -
175C LYS* 2.6 27.1 + - - +
176C TRP* 3.0 30.5 - - + -
56L ASP* 3.5 10.3 - - - +
57L ALA* 3.3 21.5 + - - -
58L ARG* 4.2 14.7 + - - +
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Residues in contact with TRP 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* 4.1 0.2 - - - +
48C ASP* 1.3 81.9 - - + +
50C VAL* 1.3 67.0 + - - +
51C GLN* 3.0 47.1 - - + -
92C GLU* 4.3 21.0 + - - +
93C PHE* 5.3 7.6 - + - -
162C ARG* 3.9 23.3 - - + -
163C ALA* 3.0 5.4 - - - +
164C TYR* 2.7 80.1 + + + +
166C LYS* 5.3 5.6 - - - +
54L VAL* 3.4 37.4 - - + +
55L PHE 3.8 2.7 - - - -
56L ASP* 4.7 1.1 - - - +
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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* 3.7 13.9 - - + -
48C ASP 4.2 0.2 - - - -
49C TRP* 1.3 80.1 - - - +
51C GLN* 1.3 66.1 + - - +
52C ILE* 4.2 15.3 - - + -
64C ILE* 5.8 0.2 - - + -
65C ALA* 4.4 20.4 - - + +
68C LEU* 3.8 28.7 - - + -
161C LEU* 4.4 4.7 - - + -
162C ARG 3.2 9.2 - - - +
163C ALA* 3.7 16.8 - - + -
54L VAL* 3.7 0.9 - - - +
55L PHE* 2.7 50.4 + - - +
57L ALA* 4.9 3.6 - - + -
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Residues in contact with GLN 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 TRP* 3.0 38.0 - - + -
50C VAL* 1.3 74.2 - - - +
52C ILE* 1.3 64.7 + - - +
53C ASP* 3.8 1.4 + - - +
161C LEU* 3.4 1.7 - - - +
162C ARG* 2.8 53.1 + - + +
52L LEU* 3.2 50.0 - - + +
53L VAL 3.2 23.3 - - - +
54L VAL* 4.7 4.6 - - - +
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Residues in contact with ILE 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 VAL* 4.2 16.2 - - + -
51C GLN* 1.3 80.8 - - - +
53C ASP* 1.3 64.2 + - - +
54C ALA 3.9 4.7 - - - +
55C ASN* 3.5 31.9 - - + +
61C ASP* 3.3 45.5 - - + +
64C ILE* 4.6 11.9 - - + -
65C ALA* 5.0 0.7 - - + +
159C LEU* 4.4 5.2 - - + -
160C ARG 3.9 8.1 - - - +
161C LEU* 3.9 9.0 - - + -
48L ARG* 3.2 28.8 + - - +
52L LEU* 5.7 2.4 - - - +
53L VAL 4.0 8.0 + - - +
55L PHE* 4.3 11.9 - - + -
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Residues in contact with ASP 53 (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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51C GLN* 3.8 4.9 + - - +
52C ILE* 1.3 74.4 - - - +
54C ALA* 1.3 62.2 + - - +
160C ARG* 2.8 51.7 + - + +
161C LEU* 4.6 1.6 - - - +
48L ARG* 3.7 14.3 + - - +
49L THR 5.0 4.0 - - - +
50L LYS* 5.5 3.5 - - - +
52L LEU* 5.0 15.2 - - + +
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Residues in contact with ALA 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 ILE* 4.0 1.1 - - - -
53C ASP* 1.3 87.2 - - - +
55C ASN* 1.3 61.0 + - - +
56C SER* 5.8 0.4 - - - -
158C GLU* 4.1 20.6 - - + +
159C LEU* 3.3 6.9 - - - +
160C ARG* 2.9 34.5 + - + +
48L ARG* 4.7 4.3 - - - +
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Residues in contact with ASN 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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52C ILE* 3.5 19.9 - - + +
54C ALA* 1.3 74.4 - - - +
56C SER* 1.3 62.9 + - - +
57C SER* 3.2 15.5 + - - +
59C LEU 3.7 8.6 + - - -
61C ASP* 3.0 39.8 + - - +
64C ILE* 3.3 34.8 - - - +
158C GLU 3.8 1.8 - - - -
159C LEU* 3.7 7.2 - - + +
48L ARG* 4.7 9.3 + - - +
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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