Contacts of the strand formed by residues 158 - 169 (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 GLU 158 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C ALA* 3.6 19.3 - - + +
56C SER* 2.3 50.1 + - - +
57C SER 4.3 0.7 + - - -
104C ASP* 6.1 0.2 - - - +
105C VAL 3.6 11.9 - - - +
106C ARG* 3.4 36.4 + - + +
153C LEU* 4.5 5.3 - - - +
156C GLY 4.7 5.8 - - - +
157C GLN* 1.3 71.8 - - - +
159C LEU* 1.3 62.0 + - - +
160C ARG* 6.3 2.0 - - + -
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Residues in contact with LEU 159 (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* 4.4 3.8 - - + -
54C ALA 3.3 12.8 - - - +
55C ASN* 3.7 25.6 - - + +
57C SER* 5.6 0.4 - - - -
64C ILE* 3.9 23.8 - - + -
103C LEU* 3.5 25.9 - - + +
104C ASP* 3.5 1.1 - - - -
105C VAL* 3.1 44.6 + - + +
115C VAL* 5.2 1.6 - - + -
150C ILE* 5.3 2.0 - - + -
151C VAL* 4.1 21.8 - - + -
153C LEU* 4.5 8.2 - - + +
158C GLU* 1.3 74.0 - - - +
160C ARG* 1.3 60.7 + - - +
161C LEU* 3.8 25.6 - - + -
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Residues in contact with ARG 160 (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* 3.8 1.4 - - - +
53C ASP* 2.8 59.0 + - + +
54C ALA* 2.9 23.4 + - + +
103C LEU 3.4 5.8 - - - +
104C ASP* 3.1 39.9 + - + +
106C ARG* 3.6 14.0 - - - +
158C GLU* 6.3 3.1 - - + -
159C LEU* 1.3 74.6 - - - +
161C LEU* 1.3 58.6 + - - +
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Residues in contact with LEU 161 (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* 4.4 1.3 - - + -
51C GLN 3.4 14.8 - - - +
52C ILE* 3.9 15.0 - - + -
53C ASP* 4.1 2.9 - - - +
64C ILE* 4.0 21.1 - - + -
68C LEU* 3.9 24.5 - - + -
102C THR* 3.8 3.2 + - - -
103C LEU* 3.1 56.1 + - + +
120C LEU* 5.2 2.2 - - + -
159C LEU* 3.8 30.3 - - + -
160C ARG* 1.3 78.0 - - - +
162C ARG* 1.3 78.4 + - - +
163C ALA* 4.7 4.5 - - + +
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Residues in contact with ARG 162 (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* 4.2 14.3 - - + -
50C VAL* 3.2 6.2 - - - +
51C GLN* 2.8 54.5 + - + +
93C PHE* 4.8 4.0 - - - -
100C GLU* 3.4 21.0 + - + +
101C PHE 3.8 9.0 - - - +
102C THR* 4.5 8.5 - - - +
161C LEU* 1.3 81.3 - - - +
163C ALA* 1.3 63.0 + - - +
164C TYR* 2.7 39.8 + - - -
52L LEU* 6.3 0.2 - - - +
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Residues in contact with ALA 163 (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 19.3 - - + -
49C TRP* 3.0 10.5 - - - +
50C VAL* 3.7 15.3 - - + -
68C LEU* 5.0 1.1 - - + -
100C GLU* 3.6 3.2 - - - +
101C PHE* 2.7 54.8 + - + +
120C LEU* 5.4 1.1 - - + -
161C LEU* 4.8 7.2 - - + -
162C ARG* 1.3 76.1 - - - +
164C TYR* 1.3 61.7 + - - +
165C ALA 4.1 0.4 - - - -
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Residues in contact with TYR 164 (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* 4.5 0.9 - - - +
48C ASP* 3.1 19.4 + - - +
49C TRP* 2.7 55.4 + + + +
93C PHE* 3.0 59.3 - + + -
98C SER* 4.5 13.5 - - - +
99C VAL 3.4 14.6 - - - +
100C GLU* 3.4 34.8 + - + -
162C ARG* 2.7 29.9 + - - -
163C ALA* 1.3 74.0 - - - +
165C ALA* 1.3 62.7 + - - +
166C LYS* 3.8 6.2 + - + +
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Residues in contact with ALA 165 (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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45C ILE* 3.6 20.6 - - + -
46C ALA 3.2 23.3 - - - +
47C ILE* 3.9 5.5 - - - +
73C LEU* 3.7 11.9 - - + -
82C LEU* 4.9 0.2 - - - +
98C SER* 3.5 2.4 - - - -
99C VAL* 2.8 37.8 + - + +
101C PHE* 4.0 15.5 - - + -
163C ALA 4.1 1.4 + - - -
164C TYR* 1.3 71.9 - - - +
166C LYS* 1.3 62.3 + - - +
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Residues in contact with LYS 166 (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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45C ILE* 3.6 7.6 - - - -
46C ALA 3.1 25.6 + - - +
48C ASP* 3.1 39.7 + - + +
49C TRP* 5.3 5.6 - - - +
82C LEU* 4.7 1.6 - - - -
85C SER* 3.8 33.8 + - - +
93C PHE* 6.3 1.1 - - + -
97C CYS 4.0 15.0 - - - +
98C SER* 4.2 9.0 - - - +
164C TYR* 3.8 7.8 + - + +
165C ALA* 1.3 80.3 - - - +
167C LYS* 1.3 67.4 + - - +
176C TRP* 3.3 12.1 + - + -
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Residues in contact with LYS 167 (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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43C PRO* 3.9 21.7 - - + +
44C ILE 3.2 15.5 - - - +
45C ILE* 4.5 2.5 - - + +
79C VAL* 3.5 27.0 + - + +
80C ASP* 4.2 15.4 + - - +
82C LEU* 2.9 39.9 + - + +
83C GLN* 4.2 8.2 + - - +
84C TYR* 3.3 62.8 + - + +
85C SER 5.2 2.1 + - - +
86C ARG* 5.6 1.6 + - - -
97C CYS 4.9 1.6 + - - -
166C LYS* 1.3 77.6 - - - +
168C GLY* 1.3 61.5 + - - +
176C TRP* 4.3 2.0 - - - -
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Residues in contact with GLY 168 (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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43C PRO* 3.8 1.3 - - - +
44C ILE 3.2 25.2 + - - -
84C TYR* 4.7 2.5 - - - -
86C ARG* 6.2 1.1 - - - -
167C LYS* 1.3 76.7 - - - +
169C PHE* 1.3 69.9 + - - +
172C GLU* 4.4 6.3 - - - -
176C TRP* 3.3 32.7 - - - +
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Residues in contact with PHE 169 (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 ALA 3.3 18.4 - - - +
41C GLU* 4.2 18.2 - - - +
42C VAL 3.9 12.6 - - - +
43C PRO* 4.4 3.8 - - + -
84C TYR* 4.2 27.8 - + - -
86C ARG* 4.7 4.9 - - - -
168C GLY* 1.3 82.0 - - - +
170C GLY* 1.3 60.8 + - - +
171C LYS* 3.4 39.7 - - + -
172C GLU* 2.8 32.8 + - + +
173C HIS 3.5 3.3 + - - -
176C TRP* 3.4 12.0 - - - +
10K PHE* 3.6 41.5 - + - -
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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