Contacts of the strand formed by residues 119 - 128 (chain B) in PDB entry 5HAN
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 VAL 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A GLU* 4.1 3.6 - - - +
30B MET* 4.2 10.3 - - + -
31B LYS 4.0 4.0 - - - +
32B PRO* 4.5 0.7 - - - -
33B LYS* 3.6 13.0 - - - +
42B THR* 3.8 15.7 - - + -
46B PHE* 4.4 8.3 - - + -
113B ASN 4.9 4.9 - - - +
116B MET* 3.3 55.3 + - + +
117B GLY 3.4 0.4 - - - -
118B ASP* 1.3 83.3 - - - +
120B GLU* 1.4 61.8 + - - +
121B TYR* 3.3 33.0 - - - +
122B ALA* 4.2 7.2 - - + -
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Residues in contact with GLU 120 (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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297A SER* 5.3 0.3 + - - -
299A GLN* 3.6 28.4 + - + +
332A GLU* 4.7 4.2 - - - +
31B LYS* 2.8 43.0 + - + +
32B PRO 3.9 12.9 - - - +
33B LYS* 3.4 24.8 - - + +
34B ALA* 4.8 4.3 + - - +
119B VAL* 1.4 73.2 - - - +
121B TYR* 1.3 79.8 + - + +
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Residues in contact with TYR 121 (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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299A GLN* 3.8 31.4 - - - +
29B ILE* 4.2 21.2 - - + +
30B MET* 3.4 3.8 - - - -
31B LYS* 3.0 77.5 + - + +
80B SER* 5.0 4.6 + - - -
119B VAL* 3.3 10.9 - - - +
120B GLU* 1.3 90.6 - - + +
122B ALA* 1.3 65.4 + - - +
123B LYS* 6.2 1.1 - - + -
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Residues in contact with ALA 122 (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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28B TYR* 5.0 2.2 - - + -
29B ILE 3.3 7.9 - - - -
30B MET* 4.0 13.2 - - + -
46B PHE* 3.5 35.7 - - + -
82B MET* 4.9 1.1 - - + -
110B ILE* 5.0 0.9 - - - -
113B ASN 5.5 0.4 - - - +
114B GLN* 2.9 35.7 + - - +
119B VAL* 4.2 4.5 - - + +
121B TYR* 1.3 79.1 - - - +
123B LYS* 1.3 59.3 - - - +
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Residues in contact with LYS 123 (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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28B TYR* 3.1 5.7 - - - -
29B ILE* 2.9 34.6 + - + +
110B ILE* 4.8 1.8 - - - -
121B TYR* 5.4 1.3 - - + -
122B ALA* 1.3 75.0 - - - +
124B MET* 1.3 71.7 + - - +
125B TYR* 3.5 30.9 + - + +
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Residues in contact with MET 124 (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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26B CYS* 3.8 11.2 - - + -
27B ALA 3.5 7.6 - - - +
28B TYR* 3.8 17.3 - - + +
105B PHE* 4.1 9.2 - - + -
109B THR* 3.3 45.8 - - - +
110B ILE* 4.2 18.9 - - + +
123B LYS* 1.3 83.1 - - - +
125B TYR* 1.3 59.8 + - - +
126B ASP 3.5 25.1 - - - +
127B PHE* 4.1 23.1 - - - -
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Residues in contact with TYR 125 (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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27B ALA* 2.9 13.4 + - + +
29B ILE* 3.5 40.2 - - + +
123B LYS* 3.5 41.8 + - + +
124B MET* 1.3 74.6 - - - +
126B ASP* 1.3 65.4 + - + +
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Residues in contact with ASP 126 (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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26B CYS* 3.5 0.3 - - - -
27B ALA* 3.0 36.7 + - + +
124B MET* 3.5 10.2 - - - +
125B TYR* 1.3 80.7 - - + +
127B PHE* 1.3 91.8 + - - +
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Residues in contact with PHE 127 (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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24B VAL* 5.0 0.9 - - + -
25B LEU 3.1 13.2 - - - +
26B CYS* 4.0 7.0 - - - -
102B ILE* 5.6 7.4 - - + -
105B PHE* 3.7 42.6 - + + -
124B MET* 4.1 8.3 - - - -
126B ASP* 1.3 93.6 + - - +
128B TYR* 1.3 66.9 + - - +
129B VAL* 4.4 20.0 + - + +
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Residues in contact with TYR 128 (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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17B LEU 5.6 0.2 - - - -
18B ILE* 3.8 43.8 + - + +
21B GLY* 5.9 0.2 - - - -
23B HIS 4.1 10.5 - - - -
24B VAL* 3.4 13.2 - - - +
25B LEU* 2.7 54.9 + - + -
127B PHE* 1.3 75.2 - - - +
129B VAL* 1.3 73.0 + - - +
130B PRO* 3.7 28.1 - - + +
131B PRO* 4.0 9.5 - - - +
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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