Contacts of the strand formed by residues 134 - 140 (chain C) in PDB entry 5MLE
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 ASP 134 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C THR 3.9 8.9 + - - +
103C MET* 3.6 7.2 - - - -
104C ILE 3.5 9.2 + - - -
133C CYS* 1.3 91.8 - - - +
135C TYR* 1.3 61.9 + - - +
398C LYS* 2.9 25.0 + - - +
408C ASP* 4.3 2.8 - - - +
448C SER* 4.8 2.6 + - - -
449C GLN* 3.6 17.7 + - - +
467C ARG* 2.8 64.6 + - - +
469C ILE* 4.0 11.4 - - + -
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Residues in contact with TYR 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C PHE* 5.2 1.1 - + - -
103C MET* 3.7 6.0 - - - +
104C ILE* 3.2 34.1 - - + +
124C ARG* 3.5 14.4 + - - -
127C ALA* 3.3 33.7 - - + +
128C ASP* 3.0 33.5 + - - -
131C SER* 4.2 13.5 - - - +
133C CYS 4.2 3.1 - - - +
134C ASP* 1.3 78.3 - - - +
136C SER* 1.3 69.3 + - - +
137C LEU* 4.1 16.4 - - + -
466C GLY 4.5 4.3 - - - -
467C ARG 3.1 15.2 + - - +
468C TYR* 3.5 36.4 - + - -
469C ILE* 2.8 30.7 + - - +
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Residues in contact with SER 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C MET* 3.7 13.2 - - - -
104C ILE 3.0 5.9 + - - +
105C ILE* 3.4 13.8 - - - -
106C ASP 3.0 21.8 + - - -
135C TYR* 1.3 81.9 - - - +
137C LEU* 1.3 70.5 + - - +
468C TYR* 3.7 13.9 - - - -
469C ILE 2.6 25.0 + - - -
471C ARG* 3.2 21.8 + - - -
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Residues in contact with LEU 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C PHE* 5.2 1.6 - - + -
105C ILE* 4.2 0.2 - - - +
106C ASP* 3.5 24.0 - - + +
108C VAL* 3.8 29.8 - - + -
120C PHE* 3.8 25.1 - - + -
123C TRP* 4.0 20.4 - - + +
124C ARG* 4.0 17.5 - - + +
135C TYR* 4.1 13.2 - - + -
136C SER* 1.3 88.7 + - - +
138C HIS* 1.3 60.2 + - - +
139C VAL* 3.9 0.7 + - - +
161C VAL* 4.1 9.4 - - - +
468C TYR* 3.8 18.0 - - + +
471C ARG* 2.4 27.6 + - - +
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Residues in contact with HIS 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C VAL 2.9 28.5 - - - -
105C ILE* 3.2 23.6 - - + +
106C ASP 2.8 9.9 + - - +
107C HIS* 3.1 30.9 + - - +
108C VAL* 2.9 29.1 + - - +
137C LEU* 1.3 73.9 - - - +
139C VAL* 1.3 60.7 + - - +
140C ASP* 4.2 0.9 - - - +
163C SER* 3.1 33.2 - - - +
164C PHE* 5.7 0.2 - - - -
196C GLN* 3.6 22.4 + - - +
392C PHE* 3.9 18.7 - + - -
471C ARG* 3.9 3.1 + - - -
608C NI 3.3 11.9 - - + -
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Residues in contact with VAL 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C VAL* 3.9 19.5 - - + +
110C PRO* 5.1 0.9 - - + -
116C LEU* 4.2 24.7 - - + +
120C PHE* 4.6 9.9 - - + -
137C LEU 4.4 0.9 - - - +
138C HIS* 1.3 77.3 - - - +
140C ASP* 1.3 74.8 + - - +
141C ILE* 3.9 0.4 + - + -
155C LEU* 4.2 12.8 - - + -
161C VAL* 4.0 29.6 - - + -
163C SER 3.3 6.9 + - - -
164C PHE* 3.2 27.0 - - + +
165C LEU* 3.1 20.9 + - - -
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Residues in contact with ASP 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ARG* 3.0 20.4 + - - -
107C HIS* 2.6 29.1 + - - +
108C VAL 2.8 18.7 + - - +
109C VAL* 3.8 9.8 - - + +
110C PRO* 3.1 26.5 - - + +
116C LEU* 4.4 0.5 - - - +
139C VAL* 1.3 79.1 - - - +
141C ILE* 1.3 62.5 + - - +
142C SER* 6.3 0.2 - - - -
165C LEU* 3.4 20.8 - - - +
167C TYR* 2.5 35.9 + - + +
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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