Contacts of the strand formed by residues 173 - 186 (chain C) in PDB entry 4LDD
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 173 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C THR* 3.7 28.7 + - - +
47C PRO 4.4 6.9 + - - -
48C SER* 4.7 0.3 + - - -
81C VAL* 3.7 3.3 - - - -
82C ILE* 2.9 60.3 + - + +
83C SER* 5.5 0.2 - - - -
84C GLY 5.5 4.0 - - - +
122C ILE 5.5 0.2 + - - -
124C HIS* 5.2 1.1 - - - -
172C PHE* 1.3 79.4 - - - +
174C PHE* 1.3 77.9 + - - +
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Residues in contact with PHE 174 (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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48C SER* 3.4 33.2 - - - -
49C ASN* 4.0 1.6 + - - +
79C VAL* 3.5 28.3 - - + -
80C ASN 3.9 1.3 - - - -
81C VAL* 4.2 15.5 - - + -
82C ILE* 4.8 4.0 - - - +
94C ILE* 3.6 19.3 - - + -
122C ILE* 3.5 33.4 + - + -
124C HIS* 3.5 34.8 - + + -
133C VAL* 3.9 23.3 - - + -
163C LEU* 4.7 8.7 - - + -
172C PHE* 4.0 14.8 - + - -
173C THR* 1.3 88.8 + - - +
175C ASP* 1.3 60.8 + - - +
176C LEU 5.0 0.2 - - - +
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Residues in contact with ASP 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ASN* 3.5 19.8 + - - +
79C VAL* 4.3 1.3 - - - -
80C ASN* 2.9 55.6 + - + +
82C ILE* 4.4 18.3 - - + +
174C PHE* 1.3 72.9 - - - +
176C LEU* 1.3 62.1 + - - +
177C THR* 3.2 14.9 + - - +
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C SER* 4.5 6.2 - - - +
49C ASN* 2.8 40.3 + - - +
51C LEU* 3.6 37.2 - - + +
77C ALA* 3.9 11.7 - - + -
78C MET 4.2 0.4 - - - -
79C VAL* 3.7 25.3 - - + +
120C TYR* 3.9 19.7 - - + +
122C ILE* 4.7 14.6 - - + -
174C PHE* 4.0 1.0 - - + -
175C ASP* 1.3 69.4 - - - +
177C THR* 1.3 60.9 + - - +
178C ALA 3.6 23.3 - - - +
179C LEU* 4.8 11.9 - - + -
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Residues in contact with THR 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 3.8 8.0 - - - +
78C MET* 2.4 32.9 + - - +
80C ASN* 3.6 20.0 - - - +
91C GLN* 2.8 30.7 + - - +
175C ASP* 3.2 21.1 + - - +
176C LEU* 1.3 73.6 - - - +
178C ALA* 1.3 64.0 + - - +
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Residues in contact with ALA 178 (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 LEU* 3.8 7.8 - - - +
54C ILE* 5.2 10.5 - - + -
76C GLU 4.6 0.7 - - - -
77C ALA* 3.5 3.1 - - - -
78C MET* 2.9 40.6 + - + -
91C GLN* 5.9 1.3 - - - +
176C LEU* 3.6 5.5 - - - +
177C THR* 1.3 83.8 + - - +
179C LEU* 1.3 62.2 + - - +
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Residues in contact with LEU 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 4.1 18.0 - - + +
52C ARG 4.3 4.6 + - - +
53C PRO* 3.3 22.7 - - + +
54C ILE* 2.7 41.9 + - - +
75C LEU* 4.0 31.4 - - + -
76C GLU 3.7 3.1 - - - +
77C ALA* 3.9 23.6 - - + -
96C LEU* 6.0 0.9 - - + -
120C TYR* 3.7 37.5 - - + -
122C ILE* 6.5 0.4 - - + -
176C LEU* 4.8 9.4 - - + -
178C ALA* 1.3 75.9 - - - +
180C LYS* 1.3 57.3 + - - +
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Residues in contact with LYS 180 (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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184A GLN* 5.9 2.2 - - - +
187A PRO* 5.7 1.8 - - - +
54C ILE* 3.3 12.1 - - + +
55C ALA 4.9 0.2 - - - -
56C ASP* 3.5 43.6 + - + +
57C ASP* 5.3 2.7 + - - -
75C LEU* 3.4 10.1 - - - +
76C GLU* 2.9 65.6 + - + +
179C LEU* 1.3 74.0 - - - +
181C LEU* 1.3 62.5 + - - +
182C ILE* 3.8 15.2 + - + +
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Residues in contact with LEU 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 5.8 2.5 - - + -
53C PRO* 4.7 1.8 - - + +
54C ILE 2.9 11.9 + - - +
55C ALA* 4.7 2.0 - - - -
56C ASP* 3.2 25.5 + - - +
59C ILE* 3.4 11.2 - - + +
73C PHE* 4.4 17.7 - - + -
74C ILE 3.5 21.5 - - - +
75C LEU* 3.7 17.0 - - + -
98C LEU* 4.7 0.4 - - + -
112C THR* 4.7 11.2 - - + -
115C ILE* 3.9 28.0 - - + -
116C MET* 3.6 36.6 - - + -
179C LEU 4.3 0.2 + - - -
180C LYS* 1.3 72.7 - - - +
182C ILE* 1.3 69.1 + - - +
183C THR* 5.4 2.5 - - + -
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Residues in contact with ILE 182 (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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184A GLN* 4.2 19.5 - - - +
56C ASP* 4.3 14.6 - - - +
58C THR* 5.3 2.7 - - - +
59C ILE* 5.9 0.4 - - + -
72C ALA 3.9 0.2 - - - +
73C PHE* 3.7 1.4 - - - -
74C ILE* 2.8 50.8 + - + +
76C GLU* 3.4 31.0 - - + +
95C TRP* 4.0 26.0 - - + -
180C LYS* 3.8 21.8 - - + +
181C LEU* 1.3 79.0 - - - +
183C THR* 1.3 71.1 + - - +
184C GLN* 6.1 0.9 - - + -
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Residues in contact with THR 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ILE* 3.7 38.8 - - + +
64C HIS* 3.0 35.2 + - + +
71C SER* 4.1 1.6 - - - -
72C ALA 3.1 13.5 + - - -
73C PHE* 3.9 12.3 - - - -
74C ILE* 5.6 0.7 - - - -
108C PHE* 3.7 15.8 - - + -
181C LEU* 5.4 2.9 - - + -
182C ILE* 1.3 83.7 - - - +
184C GLN* 1.3 67.4 + - - +
185C PRO* 4.3 1.0 - - - +
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Residues in contact with GLN 184 (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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56A ASP* 5.0 7.7 + - - -
58A THR* 5.6 4.0 + - - +
76A GLU* 5.0 1.8 + - - -
95A TRP* 3.9 36.1 - - + -
180A LYS* 5.8 2.8 - - - +
182A ILE* 4.4 21.0 - - + +
64C HIS* 3.8 4.0 - - - -
71C SER* 3.5 0.2 - - - -
72C ALA* 2.8 37.0 + - + +
74C ILE* 5.3 2.4 - - + +
182C ILE* 6.1 0.7 - - + -
183C THR* 1.3 81.1 + - - +
185C PRO* 1.3 88.8 + - - +
186C LEU* 3.8 2.4 + - + +
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Residues in contact with PRO 185 (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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76A GLU* 4.7 0.9 - - - +
63C SER* 4.1 29.6 - - - +
64C HIS* 3.4 28.2 - - + +
69C VAL* 4.3 7.4 - - + -
70C SER 4.0 4.5 - - - +
71C SER* 4.6 0.2 - - - -
183C THR 4.3 1.3 - - - +
184C GLN* 1.3 109.8 + - - +
186C LEU* 1.3 67.8 + - - +
187C PRO* 4.1 4.4 - - - +
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Residues in contact with LEU 186 (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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76A GLU* 3.8 24.9 - - + +
93A PRO* 4.0 25.8 - - + +
95A TRP* 3.8 33.9 - - + -
69C VAL* 3.7 9.8 - - - +
70C SER* 2.8 39.6 + - - +
71C SER 4.5 5.2 - - - -
72C ALA* 4.5 5.6 - - + -
100C VAL* 3.8 30.3 - - + -
184C GLN* 4.0 7.2 - - + +
185C PRO* 1.3 85.6 - - - +
187C PRO* 1.3 69.1 - - + +
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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