Contacts of the strand formed by residues 125 - 132 (chain F) in PDB entry 3HEI
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 125 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F HIS* 1.3 76.2 - - - +
126F TYR* 1.3 73.1 + - - +
127F TYR* 3.9 20.1 - - - -
144F LYS* 3.8 19.7 - - - -
145F VAL 3.1 8.7 - - - -
146F THR* 2.8 27.7 + - - +
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Residues in contact with TYR 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F LEU* 4.6 6.5 - - + -
72F VAL 5.3 0.4 - - - -
108F PHE* 4.2 8.7 - + + -
118F LYS* 3.7 31.6 - - - -
119F GLU 4.1 2.5 + - - -
120F PHE* 3.6 34.7 - + + -
121F LYS* 2.8 31.6 + - - +
124F HIS* 3.3 39.3 + - + +
125F SER* 1.3 79.5 - - - +
127F TYR* 1.3 74.5 + - - +
128F TYR* 5.4 0.9 - - + -
144F LYS* 3.5 0.2 - - - -
145F VAL* 2.7 37.9 + - + +
147F VAL* 3.8 18.6 - - + -
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Residues in contact with TYR 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F LEU* 3.3 9.2 - - - +
72F VAL* 3.0 42.2 + - + +
73F GLU* 4.6 0.9 - - - -
74F HIS* 3.6 46.3 - + + +
77F TYR* 3.3 54.7 - + + -
125F SER* 3.9 25.4 - - - -
126F TYR* 1.3 82.7 - - - +
128F TYR* 1.3 64.2 + - - +
143F LEU 3.4 3.1 - - - -
144F LYS* 3.7 38.9 + - + -
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Residues in contact with TYR 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F TRP* 3.8 19.5 - - + -
47F VAL* 4.0 3.5 - - + +
49F ILE* 4.1 22.7 - - + -
69F LEU* 5.5 4.9 - - + -
70F TYR 3.2 17.3 - - - +
71F LEU* 4.1 21.9 - - + +
77F TYR* 4.2 0.9 - - - -
89F ARG* 4.2 15.3 - - + -
104F LEU* 4.6 2.0 - - + -
106F GLU* 2.7 45.1 + - + +
108F PHE* 3.6 11.2 - + - -
120F PHE* 4.5 0.2 - - - -
126F TYR 5.5 0.7 - - - -
127F TYR* 1.3 74.3 - - - +
129F ILE* 1.4 68.3 + - - +
142F ARG* 3.2 2.8 - - - +
143F LEU* 2.9 49.9 + - + +
145F VAL* 3.9 23.6 - - + -
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Residues in contact with ILE 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F TRP* 4.0 4.1 - - - -
69F LEU* 3.7 2.8 - - - +
70F TYR* 2.9 40.6 + - + -
72F VAL* 3.9 15.7 - - + -
76F GLU 4.0 3.1 - - - +
77F TYR* 3.8 29.4 - - + +
80F CYS* 3.9 10.1 - - - +
81F GLN* 3.5 16.4 - - - +
82F PRO* 3.4 42.0 - - + -
128F TYR* 1.4 79.7 - - - +
130F SER* 1.3 62.6 + - - +
141F LEU 3.5 11.0 - - - +
142F ARG* 3.8 11.7 - - + +
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Residues in contact with SER 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F TRP* 2.9 33.2 + - - -
67F TYR* 3.6 21.0 - - - -
68F ILE 3.0 12.8 - - - -
69F LEU* 4.1 2.9 - - - -
70F TYR* 4.4 2.5 - - - -
80F CYS* 4.9 6.9 - - - +
129F ILE* 1.3 79.0 - - - +
131F LYS* 1.3 74.3 + - - +
132F PRO* 4.6 1.0 - - - +
139F ARG 5.7 0.9 - - - +
141F LEU* 3.2 24.7 + - - +
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Residues in contact with LYS 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F TYR* 3.4 4.9 - - - -
68F ILE* 2.8 42.3 + - + +
70F TYR* 3.8 27.4 - - + +
80F CYS 3.3 19.0 + - - -
81F GLN* 3.1 30.4 + - - +
82F PRO* 3.6 16.4 - - + -
130F SER* 1.3 82.0 - - - +
132F PRO* 1.3 80.0 - - + +
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Residues in contact with PRO 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F GLN 3.6 6.3 - - - +
67F TYR* 3.8 10.7 - - + -
68F ILE* 5.3 2.1 - - - +
130F SER 4.6 1.1 - - - +
131F LYS* 1.3 100.1 - - + +
133F ILE* 1.3 61.4 + - - +
134F HIS* 3.5 27.2 - - + +
137F GLU 3.4 28.0 - - - +
138F ASP* 4.0 18.4 - - - +
139F ARG 5.5 5.2 - - - +
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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