Contacts of the strand formed by residues 85 - 96 (chain B) in PDB entry 5C58
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 LEU 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B PHE* 3.9 27.1 - - + -
55B TYR* 5.5 2.0 - - + -
73B LEU* 4.0 25.4 - - + -
74B THR 3.8 14.4 - - - +
75B TYR* 4.4 5.6 - - + -
84B THR* 1.3 75.3 - - - +
86B TYR* 1.3 57.5 + - - +
122B SER* 4.8 0.5 - - - -
132B VAL* 3.3 26.0 - - + +
133B HIS* 3.3 20.0 + - + +
136B VAL* 3.7 43.7 - - + -
200B HEM 4.0 26.7 - - + -
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Residues in contact with TYR 86 (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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73B LEU* 3.7 6.2 - - - +
74B THR* 3.0 60.3 + - + +
75B TYR 5.2 0.2 - - - -
76B THR* 3.5 29.8 - - + +
84B THR* 4.2 6.3 - - + -
85B LEU* 1.3 76.2 - - - +
87B GLY* 1.3 64.7 + - - +
122B SER* 3.9 9.9 - - - +
123B LEU* 3.5 25.4 - - - +
124B GLN* 3.5 47.5 + - + -
132B VAL* 5.0 0.4 - - - -
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Residues in contact with GLY 87 (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 ASN* 3.3 12.3 - - - -
73B LEU* 4.5 2.5 - - - -
74B THR* 5.0 0.9 - - - -
86B TYR* 1.3 85.5 - - - +
88B GLN* 1.3 65.2 + - - +
89B LEU 3.9 1.5 + - - -
121B SER* 3.8 1.8 + - - -
122B SER* 3.0 35.6 + - - +
132B VAL* 4.0 3.5 - - - +
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Residues in contact with GLN 88 (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 GLY* 3.4 2.5 - - - -
72B ASN* 3.0 49.4 + - + +
73B LEU* 3.7 3.9 - - - +
87B GLY* 1.3 74.2 - - - +
89B LEU* 1.3 64.1 + - - +
90B ASP* 3.4 6.1 + - + -
120B LEU 3.5 9.4 - - - +
121B SER* 4.9 10.3 + - - +
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Residues in contact with LEU 89 (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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69B ALA* 4.1 19.1 - - + -
70B GLY 3.7 7.9 - - - +
73B LEU* 4.2 8.9 - - + +
87B GLY 3.9 2.8 + - - -
88B GLN* 1.3 68.8 - - - +
90B ASP* 1.3 57.7 + - - +
91B SER 3.5 24.5 - - - +
92B LEU* 5.3 7.4 - - + -
118B LEU* 3.9 9.9 - - + +
119B ASN* 3.6 4.0 + - - -
120B LEU* 2.9 57.5 + - + +
132B VAL* 3.7 29.3 - - + +
135B VAL* 4.2 24.9 - - + -
136B VAL* 5.1 5.2 - - + -
147B LEU* 6.2 0.9 - - + -
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Residues in contact with ASP 90 (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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70B GLY 3.0 6.0 + - - -
71B GLY* 3.7 19.9 - - - +
88B GLN* 3.4 4.0 + - + +
89B LEU* 1.3 74.5 - - - +
91B SER* 1.3 64.4 + - - +
117B GLY* 3.1 19.9 + - - -
118B LEU* 2.9 27.8 + - - +
119B ASN* 4.5 5.9 + - - +
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Residues in contact with SER 91 (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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68B VAL 5.2 0.3 + - - -
69B ALA* 3.9 0.5 - - - -
70B GLY* 3.2 37.5 + - - -
89B LEU* 3.5 13.5 - - - +
90B ASP* 1.3 83.0 - - - +
92B LEU* 1.3 65.7 + - - +
93B SER* 6.5 0.2 - - - -
115B PHE 3.7 12.1 - - - -
116B GLY* 4.6 4.7 - - - -
117B GLY 5.1 0.4 - - - -
118B LEU* 3.7 4.5 - - - -
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Residues in contact with LEU 92 (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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67B PHE* 3.8 25.1 - - + -
68B VAL 3.4 17.5 - - - +
69B ALA* 4.0 12.3 - - + -
89B LEU* 5.3 7.0 - - + -
91B SER* 1.3 80.1 + - - +
93B SER* 1.3 55.8 + - - +
94B PHE* 3.6 26.9 - - + -
115B PHE* 2.8 46.7 + - + +
118B LEU* 4.5 10.8 - - + -
135B VAL* 4.7 7.4 - - + -
136B VAL* 6.3 0.4 - - + -
139B LEU* 3.9 13.7 - - + -
147B LEU* 3.9 26.2 - - + -
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Residues in contact with SER 93 (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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67B PHE* 3.4 5.2 - - - +
68B VAL* 3.1 40.5 + - - +
92B LEU* 1.3 74.3 - - - +
94B PHE* 1.3 65.0 + - - +
108B ILE* 3.9 18.6 - - - +
111B PRO* 6.2 1.8 - - - -
113B VAL 3.6 6.7 - - - -
114B SER* 3.7 21.8 - - - -
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Residues in contact with PHE 94 (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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19B TYR* 3.6 24.0 - + + +
20B LEU* 4.6 6.1 - - + -
23B TRP* 3.6 32.3 - + - +
66B ALA 4.1 3.6 - - - -
67B PHE* 3.7 17.9 - - + -
92B LEU* 3.6 36.6 - - + -
93B SER* 1.3 78.0 - - - +
95B GLY* 1.3 59.0 + - - +
108B ILE* 3.8 8.8 - - - +
111B PRO* 3.6 7.6 - - - +
112B ASP 3.3 18.3 + - - -
113B VAL* 2.7 24.2 + - + +
115B PHE* 3.9 27.8 - + - -
139B LEU* 4.0 19.5 - - + -
147B LEU* 3.8 14.4 - - + -
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Residues in contact with GLY 95 (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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19B TYR* 4.2 1.9 + - - -
23B TRP* 4.2 3.4 - - - +
65B THR* 3.9 3.9 - - - +
66B ALA* 3.1 28.3 + - - +
94B PHE* 1.3 79.7 - - - +
96B ASP* 1.3 68.8 + - - +
108B ILE* 3.7 6.7 - - - +
110B VAL 3.3 11.9 - - - -
112B ASP* 3.9 14.4 - - - -
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Residues in contact with ASP 96 (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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542A ARG* 3.8 16.0 + - - +
543A LEU* 3.7 32.5 + - + +
544A THR* 3.3 25.8 + - - +
23B TRP* 5.7 1.2 - - - -
64B VAL* 3.9 4.7 - - + +
65B THR* 3.6 19.5 + - - +
66B ALA 5.3 0.4 - - - -
95B GLY* 1.3 80.3 - - - +
97B GLY* 1.3 68.3 + - - +
108B ILE* 3.5 1.2 - - - +
109B GLN* 3.9 0.7 - - - +
110B VAL* 3.0 42.1 + - + +
112B ASP* 4.4 6.0 - - - +
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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