Contacts of the strand formed by residues 100 - 108 (chain H) in PDB entry 6AHU
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 CYS 100 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26H LEU* 5.1 5.8 - - - -
27H GLU 3.3 17.9 - - - -
28H PHE* 3.6 33.2 - - + +
43H LEU* 6.4 1.6 - - - -
92H LEU* 3.4 36.3 - - + +
93H GLY 6.1 0.2 - - - -
94H SER* 4.5 15.4 - - - -
98H LYS 3.7 4.9 + - - +
99H LYS* 1.3 75.7 - - - +
101H ALA* 1.3 89.6 + - - +
195J LEU* 4.2 11.0 + - - +
198J ARG* 3.7 0.3 + - - -
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Residues in contact with ALA 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H LEU* 4.3 4.0 - - - +
27H GLU* 3.4 28.8 + - + +
92H LEU* 5.0 1.3 - - - -
100H CYS* 1.3 92.8 - - - +
102H PHE* 1.3 61.7 + - - +
103H ARG* 4.2 16.8 - - + +
195J LEU* 4.2 21.8 - - + -
198J ARG* 3.5 22.4 - - - +
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Residues in contact with PHE 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H MET* 4.7 10.8 - - + -
24H VAL* 3.6 41.1 - - + -
25H CYS 3.9 7.4 - - - -
26H LEU* 3.7 19.7 - - + -
40H PHE* 5.0 4.3 - + - -
43H LEU* 6.4 1.3 - - + -
75H LEU* 5.5 0.7 - - + -
85H LEU 5.4 1.1 - - - -
86H TRP* 6.0 2.5 - - - -
89H LEU* 3.3 63.3 - - + +
90H THR* 5.6 0.4 - - - -
92H LEU* 6.0 1.6 - - - -
100H CYS* 6.0 0.2 - - - -
101H ALA* 1.3 75.0 - - - +
103H ARG* 1.3 62.1 + - - +
104H VAL* 3.6 28.4 + - + +
198J ARG* 3.3 26.5 + - - +
202J ASP* 5.0 7.3 - - - +
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Residues in contact with ARG 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H CYS* 3.1 41.4 + - + +
26H LEU 6.0 0.2 - - - -
27H GLU* 2.7 47.3 + - + +
101H ALA* 4.2 8.1 + - + +
102H PHE* 1.3 83.0 - - - +
104H VAL* 1.3 62.2 + - - +
105H ILE* 4.7 2.6 - - + +
24J THR* 3.4 33.5 - - - +
27J HIS* 4.7 5.7 - - - -
28J LEU* 3.6 40.6 - - + +
195J LEU* 3.4 19.3 - - - +
197J ILE* 3.1 35.2 + - - +
198J ARG* 4.7 3.8 - - - -
199J GLY* 4.8 6.1 - - - +
202J ASP* 6.3 0.4 - - - -
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Residues in contact with VAL 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H MET* 4.4 11.2 - - + -
23H LYS 4.0 11.9 - - - +
25H CYS 5.3 0.2 - - - +
86H TRP* 5.4 3.1 - - + +
102H PHE* 3.6 31.0 - - + -
103H ARG* 1.3 72.5 - - - +
105H ILE* 1.3 67.9 + - - +
106H GLN* 4.0 7.2 - - - +
107H VAL* 3.7 29.8 - - + -
119H ARG* 5.5 1.4 + - - -
28J LEU* 6.1 0.7 - - - +
199J GLY* 6.0 1.2 - - - +
201J TYR* 5.8 8.0 - - + +
202J ASP* 4.1 29.1 - - + +
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Residues in contact with ILE 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H LYS* 3.8 44.1 + - + +
25H CYS* 3.8 34.1 - - + +
103H ARG* 3.8 2.9 + - + +
104H VAL* 1.3 80.6 - - - +
106H GLN* 1.3 68.6 + - + +
117H ASN* 4.9 2.5 - - - +
118H SER* 5.4 0.5 - - - -
119H ARG* 3.8 56.7 - - + +
201J TYR* 5.3 8.7 - - - -
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Residues in contact with GLN 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H MET* 4.0 0.2 - - - -
23H LYS* 3.1 62.7 + - + +
104H VAL* 3.8 2.1 - - - +
105H ILE* 1.3 84.5 - - + +
107H VAL* 1.3 67.6 + - - +
108H SER* 4.3 0.7 - - - -
114H LEU* 2.4 43.5 + - + +
115H SER 4.9 1.0 + - - -
116H GLY 5.1 0.2 - - - -
117H ASN* 3.2 8.5 - - - +
118H SER* 2.8 51.4 + - - +
119H ARG 5.0 0.2 - - - +
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Residues in contact with VAL 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H HIS* 5.4 2.0 - - + +
21H TYR 3.7 12.3 - - - +
22H MET* 3.8 17.7 - - + -
82H LEU* 4.3 13.0 - - + -
86H TRP* 3.6 37.0 - - + +
104H VAL* 3.7 20.6 - - + -
106H GLN* 1.3 80.2 - - - +
108H SER* 1.3 66.9 + - - +
109H PRO* 5.9 0.4 - - + -
333L LYS 4.2 9.1 - - - +
334L GLY* 3.8 22.9 - - - -
335L GLY 4.4 0.5 + - - -
336L GLU* 4.5 3.2 - - - +
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Residues in contact with SER 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H HIS* 5.0 0.7 - - - -
21H TYR* 2.9 26.3 + - - +
106H GLN* 6.4 0.7 - - - -
107H VAL* 1.3 78.6 - - - +
109H PRO* 1.3 68.7 - - - +
110H PHE 3.0 23.8 + - - -
113H ALA* 4.0 11.0 - - - -
114H LEU* 3.3 22.1 + - - +
118H SER* 5.8 0.4 - - - -
335L GLY 5.4 0.7 - - - +
336L GLU* 3.5 24.5 - - - -
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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