Contacts of the strand formed by residues 76 - 83 (chain B) in PDB entry 4I9X
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 MSE 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B TRP* 3.4 7.1 - - - +
75B PRO* 1.3 89.0 - - + +
77B VAL* 1.3 69.4 + - - +
94B ILE* 3.5 23.8 - - + -
95B LEU 3.3 10.5 - - - +
97B ALA* 3.7 3.3 - - - +
103B LEU* 3.7 20.4 - - + -
146B ARG* 3.1 34.9 + - + +
147B ASN* 3.6 32.5 - - - +
148B TYR* 3.6 40.4 - - + +
110C LEU* 4.0 8.1 - - + -
114C LEU* 4.7 4.3 - - + -
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B VAL* 4.9 1.3 - - + -
72B HIS* 3.9 6.1 - - - +
76B MSE 1.3 79.9 - - - +
78B SER* 1.3 64.1 + - - +
94B ILE* 3.4 2.3 - - - +
95B LEU* 2.8 53.6 + - + +
96B ASP 4.6 0.9 - - - +
97B ALA* 3.9 20.9 - - + +
118B PHE* 4.8 4.9 - - + -
125B GLN* 6.5 0.2 - - + -
127B PHE* 3.7 37.7 - - + -
144B VAL 3.4 9.0 - - - +
145B LEU* 3.8 23.8 - - + -
146B ARG* 4.3 3.4 - - - -
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Residues in contact with SER 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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77B VAL* 1.3 79.1 - - - +
79B ILE* 1.3 64.7 + - - +
92B GLU* 2.7 33.0 + - - +
93B LEU 3.1 13.7 - - - -
94B ILE* 3.9 11.4 - - - -
95B LEU* 5.7 0.4 - - - -
127B PHE* 3.6 10.0 - - - -
142B GLU 3.7 1.6 - - - +
144B VAL* 3.0 47.7 + - - +
146B ARG* 4.4 3.9 - - - +
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Residues in contact with ILE 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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65B ILE* 4.4 11.4 - - + +
67B CYS* 4.0 11.4 - - - -
78B SER* 1.3 77.7 - - - +
80B ARG* 1.3 65.5 + - - +
81B ALA 4.1 0.2 + - - -
91B ASP 3.6 2.1 - - - +
92B GLU* 3.3 3.0 - - - -
93B LEU* 3.0 44.8 + - + +
95B LEU* 5.9 1.3 - - + -
107B LEU* 4.4 4.3 - - + +
127B PHE* 3.8 21.1 - - + -
128B SER* 3.6 38.4 - - - +
129B LEU* 3.6 32.8 - - + +
141B TYR* 4.5 9.6 - - + -
142B GLU 3.4 8.7 - - - +
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Residues in contact with ARG 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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37B ASP* 2.7 26.1 + - - -
38B ILE* 3.7 22.9 - - - +
41B LYS* 3.4 11.5 - - - +
78B SER 3.9 0.2 - - - -
79B ILE* 1.3 72.8 - - - +
81B ALA* 1.3 62.1 + - - +
82B ARG* 3.3 12.3 - - - +
90B SER* 3.0 27.3 + - - +
91B ASP 3.4 3.6 - - - -
92B GLU* 4.1 14.1 - - + -
141B TYR* 3.3 4.5 - - - -
142B GLU* 2.9 57.7 + - + +
144B VAL* 3.9 19.7 - - + -
153B ILE* 4.2 7.5 - - - +
233B ARG* 5.8 0.4 - - - +
303B CA 3.3 5.8 - - - -
151C GLU* 2.9 39.8 + - - -
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Residues in contact with ALA 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 ILE 5.5 0.2 - - - -
80B ARG* 1.3 74.7 - - - +
82B ARG* 1.3 61.7 + - - +
83B PHE* 3.9 19.5 - - + -
87B HIS* 3.4 4.7 - - - -
90B SER* 3.3 6.0 - - - -
91B ASP 2.7 32.1 + - - -
107B LEU* 3.6 26.9 - - + -
140B MSE 3.4 4.3 - - - +
141B TYR* 4.0 21.3 - - + -
303B CA 3.9 0.2 - - - -
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Residues in contact with ARG 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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47B TYR* 4.7 0.2 + - - -
80B ARG* 3.3 21.8 - - - +
81B ALA* 1.3 70.3 - - - +
83B PHE* 1.3 65.0 + - - +
87B HIS* 3.7 5.2 - - - -
89B GLY 3.4 18.4 - - - +
90B SER* 3.7 11.9 - - - -
139B GLY* 3.3 1.1 - - - -
140B MSE 2.8 61.5 + - + +
142B GLU* 3.0 33.7 + - - -
156B ARG* 4.6 4.9 - - - +
233B ARG* 3.4 25.1 - - - +
303B CA 3.0 13.4 - - - -
147C GLU* 2.8 47.4 + - - +
151C GLU* 3.3 13.5 + - - -
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Residues in contact with PHE 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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81B ALA* 3.9 21.3 - - + -
82B ARG* 1.3 74.5 - - - +
84B CYS* 1.3 67.4 + - - +
85B ARG 3.1 2.5 + - - +
87B HIS* 3.1 57.0 + + + +
91B ASP* 4.6 5.8 - - + -
107B LEU* 4.4 5.6 - - + -
110B ARG* 3.4 56.1 - - + +
111B LEU* 4.2 16.2 - - + -
136B ASP 3.7 12.8 - - - +
137B THR* 4.1 2.0 - - - -
138B ALA 3.4 12.3 - - - +
139B GLY* 3.9 0.4 - - - -
141B TYR* 3.5 26.5 - + - -
233B ARG* 3.7 18.2 - - - -
234B CYS* 4.6 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