Contacts of the strand formed by residues 70 - 83 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B SER 3.7 5.0 + - - -
69B VAL* 1.3 79.0 - - - +
71B SER* 1.3 61.5 + - - +
100B VAL* 5.0 9.2 - - - -
101B ALA 3.6 12.1 - - - -
102B ASP* 3.5 24.0 - - - +
103B GLN 4.8 0.2 + - - -
104B LYS* 5.9 0.5 - - - -
186B LEU* 2.8 35.2 + - - +
190B THR* 4.6 21.1 + - - -
191B TRP* 5.7 1.6 - - - -
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Residues in contact with SER 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B HIS* 3.2 36.0 + - - +
69B VAL* 4.4 5.7 + - - +
70B SER* 1.3 77.8 + - - +
72B ALA* 1.3 60.4 + - - +
73B PHE* 3.8 10.1 - - - -
100B VAL* 3.7 2.4 - - - +
101B ALA* 2.9 35.2 + - - +
103B GLN* 5.0 1.1 + - - +
108B PHE* 3.5 25.3 - - - -
183B THR* 4.1 1.3 - - - -
184B GLN 3.5 5.2 - - - -
185B PRO* 4.6 0.2 - - - +
186B LEU* 4.5 5.4 - - - +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B SER* 1.3 74.8 - - - +
73B PHE* 1.3 61.2 + - - +
74B ILE* 4.3 5.6 - - + -
99B GLY 3.4 9.9 - - - +
100B VAL* 4.5 4.5 - - + +
183B THR* 3.1 23.6 + - - -
184B GLN* 2.8 27.4 + - + +
186B LEU* 4.5 10.7 - - + +
258B ILE* 3.6 29.2 - - + -
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Residues in contact with PHE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B SER* 3.8 15.9 - - - -
72B ALA* 1.3 76.6 - - - +
74B ILE* 1.3 59.6 + - - +
97B PRO* 3.6 0.3 - - - +
98B LEU* 2.7 40.2 + - + -
99B GLY 2.9 19.8 + - - +
101B ALA* 3.7 25.4 - - + -
108B PHE* 3.4 42.0 - + - -
111B THR* 3.9 17.5 - - + -
112B THR* 4.5 6.5 - - - -
115B ILE* 3.8 18.2 - - + -
147B LEU* 3.6 29.6 - - + -
181B LEU* 4.4 12.8 - - + -
182B ILE 3.7 1.6 - - - -
183B THR* 3.9 12.1 - - - -
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ALA* 4.3 5.4 - - + +
73B PHE* 1.3 88.9 - - - +
75B LEU* 1.3 71.2 + - - +
76B GLU 4.8 0.2 - - - +
95B TRP* 3.5 54.3 - - + -
96B LEU 3.5 12.1 - - - +
97B PRO* 3.8 15.7 - - + -
98B LEU 4.0 0.2 - - - +
181B LEU* 3.5 5.5 - - - +
182B ILE* 2.8 48.3 + - + +
184B GLN* 5.3 2.9 - - + -
256B LYS* 4.7 4.0 - - + +
258B ILE* 4.3 24.7 - - + -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PRO* 4.7 3.1 - - + -
74B ILE* 1.3 74.1 - - - +
76B GLU* 1.3 60.7 + - - +
77B ALA 3.8 0.7 + - - -
94B ILE 3.1 3.3 - - - +
95B TRP* 3.9 0.3 - - - -
96B LEU* 2.7 53.0 + - + +
98B LEU* 3.7 32.8 - - + -
115B ILE* 4.7 6.3 - - + -
120B TYR* 5.0 11.7 - - + -
135B VAL* 5.0 7.4 - - + -
149B LEU* 4.1 11.9 - - + -
179B LEU* 4.0 30.5 - - + -
180B LYS 3.4 15.9 - - - +
181B LEU* 3.7 26.0 - - + -
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ILE* 4.2 0.8 + - - +
75B LEU* 1.3 70.3 - - - +
77B ALA* 1.3 59.8 + - - +
78B MET* 3.8 21.5 + - + +
93B PRO* 4.6 18.6 - - + +
94B ILE 3.6 5.8 - - - +
95B TRP* 4.9 12.8 - - + +
178B ALA 4.0 0.3 - - - +
179B LEU* 3.7 2.1 - - - -
180B LYS* 2.9 63.6 + - + +
182B ILE* 3.4 29.8 - - + +
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LEU 3.8 0.4 + - - -
76B GLU* 1.3 72.4 - - - +
78B MET* 1.3 61.6 + - - +
79B VAL* 3.7 7.2 - - + -
92B ILE 3.1 5.4 - - - +
93B PRO* 4.3 1.3 - - - -
94B ILE* 2.7 49.4 + - + +
96B LEU* 4.8 11.0 - - + -
122B ILE* 5.0 5.6 - - + -
176B LEU* 3.9 20.6 - - + -
178B ALA 3.5 4.3 - - - -
179B LEU* 3.9 13.0 - - + -
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Residues in contact with MET 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B GLU* 3.8 20.8 + - + +
77B ALA* 1.3 69.9 - - - +
79B VAL* 1.3 57.5 + - - +
91B GLN* 3.4 46.9 - - - +
92B ILE 3.5 4.0 - - - -
93B PRO* 3.4 41.5 - - + -
177B THR* 2.5 37.4 + - - +
178B ALA* 2.9 26.5 + - + +
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ALA* 3.8 6.7 - - + +
78B MET* 1.3 78.4 - - - +
80B ASN* 1.3 72.1 + - - +
81B VAL* 4.6 3.8 - - + -
91B GLN 3.3 0.7 + - - -
92B ILE* 2.8 44.9 + - + +
94B ILE* 3.6 28.3 - - + -
122B ILE* 4.9 5.4 - - + -
163B LEU* 5.8 0.4 - - + -
174B PHE* 3.5 31.9 - - + -
175B ASP 3.4 10.5 - - - +
176B LEU* 3.7 24.5 - - + -
177B THR* 4.3 0.2 - - - -
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Residues in contact with ASN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B VAL* 1.3 73.0 - - - +
81B VAL* 1.3 63.7 + - - +
82B ILE* 3.5 7.6 + - + +
87B VAL* 5.6 7.2 - - + +
89B MET 3.4 9.6 - - - +
90B LYS* 4.3 11.0 - - - +
91B GLN* 2.8 41.2 + - - +
174B PHE* 3.7 0.4 - - - -
175B ASP* 2.9 55.2 + - + +
177B THR* 3.7 17.2 - - - +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B VAL* 4.6 2.7 - - + -
80B ASN* 1.3 71.5 - - - +
82B ILE* 1.3 57.6 + - - +
88B LEU* 2.8 42.4 + - + -
89B MET* 2.9 30.1 + - + +
92B ILE* 4.2 13.4 - - + +
163B LEU* 6.3 2.2 - - + -
168B LEU* 5.1 12.3 - - + -
172B PHE* 3.5 42.0 - - + -
173B THR 3.7 3.1 - - - -
174B PHE* 4.2 25.1 - - + +
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Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ASN* 4.0 11.7 - - + +
81B VAL* 1.3 78.3 - - - +
83B SER* 1.3 59.5 + - - +
84B GLY 4.0 13.7 - - - +
85B PRO 5.7 0.9 - - - +
86B LYS 4.0 8.1 - - - +
87B VAL* 3.6 31.9 - - + -
88B LEU* 4.2 1.6 - - - +
172B PHE* 3.5 3.9 - - - +
173B THR* 2.9 61.1 + - + +
174B PHE 4.8 3.1 - - - +
175B ASP* 4.4 18.8 - - + +
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Residues in contact with SER 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ILE* 1.3 74.3 - - - +
84B GLY* 1.3 62.8 + - - +
85B PRO* 3.5 7.8 - - - +
86B LYS* 3.4 16.7 + - - +
88B LEU* 3.5 28.5 - - - +
171B TYR* 3.5 19.6 + - - +
172B PHE* 4.4 3.1 - - - +
173B 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