Contacts of the strand formed by residues 122 - 126 (chain G) in PDB entry 1MVW
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 122 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G TYR* 3.3 17.0 - - - +
119G SER 3.4 35.4 + - - +
120G GLY 3.3 0.2 - - - -
121G LEU* 1.3 86.1 - - - +
123G CYS* 1.3 60.6 + - - +
124G VAL* 3.8 11.4 - - + -
488G GLN* 5.3 0.7 - - - -
491G PHE* 3.3 44.4 - + - -
671G PHE* 3.7 24.7 - + + -
673G ARG* 3.9 27.6 - - + -
698G ASN 4.7 0.7 - - - -
699G GLY* 3.5 20.6 - - - -
700G VAL* 3.4 42.2 - - + -
703G GLY* 4.8 3.6 - - - -
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Residues in contact with CYS 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G TYR* 4.4 12.8 - - - -
117G THR 5.0 0.9 - - - -
118G TYR* 4.1 12.6 - - + -
122G PHE* 1.3 73.7 - - - +
124G VAL* 1.3 76.0 + - - +
125G THR* 4.1 0.3 + - - -
154G HIS 4.4 2.7 - - - -
155G ILE* 4.3 24.9 - - - -
158G ILE* 3.0 37.2 - - + -
671G PHE 3.5 9.6 + - - +
672G VAL* 3.8 11.4 - - + +
673G ARG 3.3 17.9 + - - +
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Residues in contact with VAL 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G MET* 4.3 5.8 - - + -
106G LEU* 4.4 20.6 - - + -
115G ILE 3.5 3.0 - - - +
116G TYR* 3.6 5.0 - - - -
117G THR* 2.9 40.8 + - + +
119G SER* 4.1 24.7 - - - +
122G PHE* 4.3 5.8 - - + -
123G CYS* 1.3 77.1 - - - +
125G THR* 1.3 63.1 + - - +
126G VAL* 4.7 4.0 - - + -
673G ARG* 3.4 6.1 - - + +
675G ILE* 3.0 36.1 - - + -
695G LEU* 6.1 0.2 - - + -
700G VAL* 4.2 16.6 - - + -
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Residues in contact with THR 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G ILE* 3.4 6.7 - - + -
116G TYR* 2.8 34.0 - - + +
123G CYS* 4.1 4.3 + - - -
124G VAL* 1.3 73.8 + - - +
126G VAL* 1.3 73.2 + - - +
127G ASN* 5.4 0.9 - - - -
128G PRO* 6.1 0.9 - - + -
135G TYR* 5.7 0.9 - - - +
155G ILE* 4.1 9.5 - - - +
183G ALA 5.3 3.6 - - - +
188G ASN* 4.1 22.4 - - - +
672G VAL* 4.9 1.1 - - - +
673G ARG 3.0 12.2 + - - -
674G CYS* 4.3 7.9 - - + -
675G ILE* 2.5 35.1 + - - +
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Residues in contact with VAL 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G LEU* 5.1 9.2 - - + +
110G TYR* 4.1 27.1 - - + -
114G MET 5.0 1.1 - - - +
115G ILE* 3.1 38.6 + - - +
117G THR* 4.9 8.1 - - + -
124G VAL* 4.7 7.4 - - + -
125G THR* 1.3 86.9 - - - +
127G ASN* 1.4 66.7 + - - +
128G PRO* 3.2 6.1 - - - +
675G ILE* 3.5 28.3 - - + +
677G PRO* 4.1 19.1 - - + -
686G MET* 5.1 8.1 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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