Contacts of the strand formed by residues 70 - 83 (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 SER 70 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A PRO* 5.7 4.9 - - - -
164A PRO* 4.7 11.2 - - - +
68C SER 3.7 5.4 + - - -
69C VAL* 1.3 76.4 - - - +
71C SER* 1.3 61.0 + - - +
100C VAL* 4.9 9.4 - - - -
101C ALA 3.6 12.6 - - - -
102C ASP* 3.5 23.3 - - - +
103C GLN* 4.8 0.6 + - - -
104C LYS* 5.9 0.5 - - - -
186C LEU* 2.8 43.1 + - - +
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Residues in contact with SER 71 (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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64C HIS* 3.2 35.4 + - - +
69C VAL* 4.3 5.4 + - - +
70C SER* 1.3 79.1 + - - +
72C ALA* 1.3 61.6 + - - +
73C PHE* 3.8 10.1 - - - -
100C VAL* 3.7 2.3 - - - +
101C ALA* 2.9 35.8 + - - +
103C GLN* 5.0 0.9 + - - +
108C PHE* 3.5 25.8 - - - -
183C THR* 4.1 1.3 - - - -
184C GLN 3.5 5.2 - - - -
185C PRO* 4.6 0.2 - - - +
186C LEU* 4.5 4.5 - - - -
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Residues in contact with ALA 72 (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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95A TRP* 3.9 45.3 - - + -
71C SER* 1.3 73.5 - - - +
73C PHE* 1.3 63.2 + - - +
74C ILE* 4.3 2.9 - - + -
99C GLY 3.4 9.4 - - - +
100C VAL* 4.5 0.7 - - - +
183C THR* 3.1 23.6 + - - -
184C GLN* 2.8 25.5 + - + +
186C LEU* 4.5 5.8 - - + +
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Residues in contact with PHE 73 (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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71C SER* 3.8 16.4 - - - -
72C ALA* 1.3 76.3 - - - +
74C ILE* 1.3 60.7 + - - +
97C PRO* 4.8 0.2 - - - +
98C LEU* 2.7 39.9 + - + -
99C GLY 2.9 20.3 + - - +
101C ALA* 3.7 24.2 - - + -
108C PHE* 3.4 43.1 - + - -
111C THR* 3.9 17.5 - - + -
112C THR* 4.5 5.8 - - - -
115C ILE* 3.8 17.3 - - + -
147C LEU* 3.7 28.9 - - + -
181C LEU* 4.4 13.0 - - + -
182C ILE 3.7 1.3 - - - -
183C THR* 3.9 11.9 - - - -
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Residues in contact with ILE 74 (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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95A TRP* 3.6 33.9 - - + +
72C ALA* 4.3 3.8 - - + +
73C PHE* 1.3 89.4 - - - +
75C LEU* 1.3 71.1 + - - +
76C GLU 4.7 0.2 - - - +
95C TRP* 3.5 51.6 - - + -
96C LEU 3.5 11.7 - - - +
97C PRO* 3.8 15.3 - - + -
98C LEU* 4.0 0.6 - - - +
181C LEU* 3.5 5.5 - - - +
182C ILE* 2.8 48.4 + - + +
184C GLN* 5.3 3.6 - - + -
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Residues in contact with LEU 75 (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 PRO* 4.7 2.9 - - + -
74C ILE* 1.3 74.8 - - - +
76C GLU* 1.3 58.9 + - - +
77C ALA 3.8 0.6 + - - -
94C ILE 3.1 4.0 - - - +
95C TRP* 4.0 0.2 - - - -
96C LEU* 2.7 52.2 + - + +
98C LEU* 3.7 33.4 - - + -
115C ILE* 4.7 6.7 - - + -
120C TYR* 5.0 9.2 - - + -
135C VAL* 5.0 9.4 - - + -
149C LEU* 4.1 11.9 - - + -
179C LEU* 4.0 31.0 - - + -
180C LYS 3.4 15.5 - - - +
181C LEU* 3.7 26.7 - - + -
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Residues in contact with GLU 76 (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* 4.8 2.1 + - - -
185A PRO 4.7 2.6 - - - +
186A LEU* 4.1 16.9 - - + +
187A PRO* 3.3 36.4 - - - +
74C ILE 4.2 0.8 + - - -
75C LEU* 1.3 70.3 - - - +
77C ALA* 1.3 59.3 + - - +
78C MET* 3.8 9.4 + - + +
93C PRO* 4.6 13.9 - - + -
94C ILE 3.6 5.4 - - - +
95C TRP* 5.0 5.2 - - + +
178C ALA 4.0 0.3 - - - +
179C LEU* 3.7 2.1 - - - -
180C LYS* 2.9 61.0 + - + +
182C ILE* 3.4 30.2 - - + +
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Residues in contact with ALA 77 (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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75C LEU 3.8 0.6 + - - +
76C GLU* 1.3 72.8 - - - +
78C MET* 1.3 60.7 + - - +
79C VAL* 3.7 7.2 - - + -
92C ILE 3.1 5.2 - - - +
93C PRO* 4.3 1.6 - - - -
94C ILE* 2.7 48.5 + - + +
96C LEU* 4.8 10.1 - - + -
122C ILE* 5.0 6.1 - - + -
176C LEU* 3.9 20.4 - - + -
178C ALA 3.5 4.5 - - - -
179C LEU* 3.9 13.0 - - + -
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Residues in contact with MET 78 (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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187A PRO* 3.5 34.5 - - + +
76C GLU* 3.8 11.3 + - + +
77C ALA* 1.3 70.5 - - - +
79C VAL* 1.3 57.3 + - - +
91C GLN* 3.4 50.7 - - - +
92C ILE 3.5 0.2 - - - -
93C PRO* 3.4 34.8 - - + -
177C THR* 2.4 37.5 + - - +
178C ALA* 2.9 25.9 + - + +
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Residues in contact with VAL 79 (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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77C ALA* 3.8 6.7 - - + +
78C MET* 1.3 77.9 - - - +
80C ASN* 1.3 73.4 + - - +
81C VAL* 4.6 4.3 - - + -
91C GLN 3.3 0.7 + - - -
92C ILE* 2.8 44.7 + - + +
94C ILE* 3.6 29.4 - - + -
122C ILE* 4.9 4.9 - - + -
163C LEU* 5.8 0.2 - - + -
174C PHE* 3.5 32.1 - - + -
175C ASP 3.4 9.6 - - - +
176C LEU* 3.7 24.9 - - + -
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Residues in contact with ASN 80 (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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79C VAL* 1.3 74.7 - - - +
81C VAL* 1.3 64.2 + - - +
82C ILE* 3.5 8.3 + - + +
87C VAL* 5.6 8.0 - - + +
89C MET 3.4 10.1 - - - +
90C LYS* 4.3 10.2 - - - +
91C GLN* 2.8 40.1 + - - +
175C ASP* 2.9 51.1 + - + +
177C THR* 3.7 17.5 - - - +
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Residues in contact with VAL 81 (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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79C VAL* 4.6 2.7 - - + -
80C ASN* 1.3 71.0 - - - +
82C ILE* 1.3 57.0 + - - +
87C VAL* 4.1 0.2 - - - -
88C LEU* 2.8 41.7 + - + -
89C MET* 2.9 29.2 + - + +
92C ILE* 4.2 13.6 - - + +
163C LEU* 6.3 1.8 - - + -
169C PRO* 5.8 2.5 - - + -
172C PHE* 3.5 42.6 - - + -
173C THR 3.7 3.6 - - - -
174C PHE* 4.2 24.5 - - + -
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Residues in contact with ILE 82 (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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80C ASN* 4.0 11.9 - - + +
81C VAL* 1.3 77.9 - - - +
83C SER* 1.3 59.4 + - - +
84C GLY 4.0 13.5 - - - +
85C PRO 5.7 1.1 - - - +
86C LYS 4.0 7.9 - - - +
87C VAL* 3.6 32.3 - - + -
88C LEU* 4.2 1.6 - - - +
172C PHE* 3.5 3.9 - - - +
173C THR* 2.9 61.0 + - + +
174C PHE 4.8 2.9 - - - +
175C ASP* 4.4 20.0 - - + +
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Residues in contact with SER 83 (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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82C ILE* 1.3 73.6 - - - +
84C GLY* 1.3 61.7 + - - +
85C PRO* 3.5 7.6 - - - +
86C LYS* 3.4 17.6 + - - +
88C LEU* 3.5 30.4 - - - +
171C TYR* 3.5 19.9 + - - +
172C PHE* 4.4 3.3 - - - +
173C THR* 5.5 0.2 - - - -
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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