Contacts of the strand formed by residues 129 - 134 (chain H) in PDB entry 4MNE
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 PHE 129 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115H LEU* 3.8 21.8 - - + -
116H GLN* 4.5 4.7 - - - -
118H LEU* 3.4 53.9 + - + +
119H HIS* 3.6 40.7 + + - -
121H CYS 5.9 0.8 + - - -
127H VAL 3.7 1.4 + - - +
128H GLY* 1.3 74.7 - - - -
130H TYR* 1.3 73.9 + - - +
131H GLY* 3.2 43.3 - - - -
132H ALA* 3.6 14.6 - - + -
141H ILE* 4.1 12.6 - - + -
142H CYS 3.7 6.3 - - - -
143H MET* 4.3 0.9 - - - +
903H 573 4.8 4.5 - - + -
904H 573 5.1 2.8 - - - -
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Residues in contact with TYR 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H VAL 4.3 5.5 + - - -
94H MET* 3.4 33.9 - - + -
119H HIS* 3.1 23.0 + - - -
128H GLY* 5.0 2.7 - - - -
129H PHE* 1.3 86.4 - - - +
131H GLY* 1.3 56.1 + - - +
142H CYS* 2.7 14.6 + - + +
143H MET 3.3 29.2 - - - -
144H GLU* 3.5 24.4 - - + +
145H HIS 4.5 1.7 + - - -
904H 573 3.0 79.8 + + + -
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Residues in contact with GLY 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H GLN* 5.5 0.9 - - - -
119H HIS* 4.7 2.7 - - - -
129H PHE* 3.2 20.5 - - - -
130H TYR* 1.3 83.1 - - - +
132H ALA* 1.3 56.3 + - - -
133H PHE* 5.3 1.8 - - - -
142H CYS* 2.7 35.9 + - - +
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Residues in contact with ALA 132 (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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112H ILE* 3.3 21.8 - - + +
115H LEU* 3.7 31.2 - - + -
116H GLN* 4.0 9.6 + - - +
129H PHE* 3.6 14.8 - - + -
131H GLY* 1.3 75.5 - - - +
133H PHE* 1.3 66.8 + - - +
140H SER 3.2 17.3 - - - +
141H ILE* 4.2 2.2 - - - -
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Residues in contact with PHE 133 (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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68H PHE* 4.0 29.4 - + - -
96H ARG* 3.9 14.6 - - - -
112H ILE* 3.5 14.3 - - + +
131H GLY 5.3 0.2 - - - -
132H ALA* 1.3 82.6 - - - +
134H TYR* 1.3 70.9 + - - +
135H SER* 4.7 6.1 - - - -
139H ILE* 3.7 0.7 - - - -
140H SER* 2.8 61.4 + - - +
142H CYS* 4.3 12.6 - - - -
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Residues in contact with TYR 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H LEU 4.7 4.7 - - - -
103H ILE* 5.3 5.0 + - + -
108H ARG* 3.3 60.2 + - + +
112H ILE* 3.9 6.8 - - + +
133H PHE* 1.3 83.9 - - - +
135H SER* 1.3 76.8 + - - +
136H ASP* 4.0 0.9 - - - -
137H GLY* 2.9 39.5 + - - -
138H GLU 3.6 11.2 - - - -
139H ILE* 3.9 20.0 - - + -
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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