Contacts of the strand formed by residues 125 - 132 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L ASN* 5.9 1.2 + - - -
36L ASP* 3.8 24.0 + - - +
38L THR* 4.0 3.3 + - - -
124P HIS* 1.3 77.9 - - - +
126P TYR* 1.3 73.2 + - - +
127P TYR* 3.8 28.4 - - - -
144P LYS* 3.7 11.3 - - - -
145P VAL 3.2 8.3 - - - -
146P THR* 2.9 26.1 + - - +
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Residues in contact with TYR 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71P LEU* 4.6 8.1 - - + -
72P VAL 5.2 0.4 - - - -
73P GLU* 6.0 1.6 - - - -
108P PHE* 4.2 8.3 - + + -
118P LYS* 3.6 31.6 - - - -
119P GLU 4.1 1.8 + - - -
120P PHE* 3.5 36.3 - + + -
121P LYS* 2.8 32.6 + - - +
124P HIS* 3.4 37.6 + - + +
125P SER* 1.3 78.9 - - - +
127P TYR* 1.3 72.5 + - - +
128P TYR* 5.5 0.7 - - + -
144P LYS* 3.4 2.3 - - - -
145P VAL* 2.7 37.3 + - + +
147P VAL* 3.8 20.9 - - + -
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Residues in contact with TYR 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L ASP* 2.6 42.8 + - - +
71P LEU* 3.3 8.7 - - - +
72P VAL* 2.9 43.9 + - + +
73P GLU* 4.6 2.0 - - - -
74P HIS* 3.6 36.0 - + + -
77P TYR* 3.3 52.0 - + + -
125P SER* 3.8 19.2 - - - -
126P TYR* 1.3 82.6 - - - +
128P TYR* 1.3 65.3 + - - +
143P LEU 3.3 2.7 - - - -
144P LYS* 3.5 33.2 + - + +
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Residues in contact with TYR 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P TRP* 3.8 20.6 - - + -
47P VAL* 4.7 3.1 - - + -
49P ILE* 4.0 25.1 - - + -
69P LEU* 5.6 4.5 - - + -
70P TYR 3.1 17.5 - - - +
71P LEU* 3.8 25.8 - - + +
77P TYR* 4.2 0.5 - - - -
89P ARG* 4.3 11.0 - - + -
104P LEU* 4.5 1.6 - - + -
106P GLU* 2.7 47.5 + - + +
108P PHE* 3.6 11.8 - + - -
120P PHE* 4.5 0.3 - - - -
126P TYR* 5.5 0.7 - - + -
127P TYR* 1.3 76.6 - - - +
129P ILE* 1.3 67.2 + - - +
142P ARG* 3.3 3.1 - - - +
143P LEU* 2.8 42.2 + - + +
145P VAL* 3.9 30.7 - - + -
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Residues in contact with ILE 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P TRP* 3.9 4.8 - - - -
69P LEU* 3.6 3.1 - - - +
70P TYR* 2.8 50.5 + - + +
72P VAL* 3.9 12.8 - - + +
76P GLU 4.2 2.5 - - - +
77P TYR* 3.8 27.8 - - + -
80P CYS* 3.7 13.0 - - - +
81P GLN 3.5 18.8 - - - +
82P PRO* 3.5 39.7 - - + -
128P TYR* 1.3 81.5 - - - +
130P SER* 1.3 58.8 + - - +
131P LYS* 4.7 3.6 - - - -
141P LEU 3.6 9.4 - - - +
142P ARG* 3.8 13.0 - - + +
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Residues in contact with SER 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P TRP* 2.9 31.9 + - - -
67P TYR* 3.6 16.9 - - - -
68P ILE 3.0 13.5 - - - -
69P LEU* 3.9 7.0 - - - -
70P TYR* 4.4 2.2 - - - -
80P CYS* 4.6 4.5 - - - -
129P ILE* 1.3 76.4 - - - +
131P LYS* 1.3 77.7 + - - +
132P PRO* 4.7 1.5 - - - +
140P CYS* 5.8 0.3 - - - -
141P LEU* 3.2 25.9 + - - +
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Residues in contact with LYS 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173I LYS* 6.3 1.2 - - - +
67P TYR* 3.3 5.4 - - - -
68P ILE* 2.8 45.1 + - + +
70P TYR* 3.9 26.6 - - + +
80P CYS* 2.7 32.9 + - - +
81P GLN* 2.7 27.4 + - - +
82P PRO* 4.1 13.7 - - + -
129P ILE* 4.7 0.9 - - - -
130P SER* 1.3 85.1 - - - +
132P PRO* 1.3 71.4 - - + +
137P GLU* 3.6 23.9 + - - +
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Residues in contact with PRO 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66P GLN 3.5 7.2 - - - +
67P TYR* 3.7 12.7 - - + -
68P ILE* 5.6 1.6 - - - +
130P SER 4.7 1.6 - - - +
131P LYS* 1.3 89.2 - - + +
133P ILE* 1.3 61.0 + - - +
134P HIS* 3.7 23.6 - - + +
135P GLN* 4.0 10.3 + - - +
136P HIS 4.4 6.1 - - - +
137P GLU* 3.6 53.3 - - + +
138P ASP 5.1 2.5 - - - +
139P ARG 5.5 4.0 - - - +
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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