Contacts of the strand formed by residues 114 - 118 (chain M) in PDB entry 4DKE
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 114 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112M ALA 3.7 2.6 + - - -
113M PRO* 1.3 70.7 - - - +
115M VAL* 1.3 60.6 + - - +
116M PHE* 3.5 22.6 - - - -
135M LEU 3.3 3.3 - - - +
136M LEU* 3.7 0.3 - - - -
137M ASN* 2.9 46.6 + - - +
138M ASN* 5.3 2.4 + - - +
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Residues in contact with VAL 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113M PRO* 3.5 20.2 + - + +
114M SER* 1.3 71.9 - - - +
116M PHE* 1.3 96.4 + - - +
134M CYS* 4.1 8.1 - - - -
135M LEU 3.4 8.5 - - - +
136M LEU* 4.9 0.9 - - + +
194M CYS* 5.0 0.9 - - + +
196M VAL* 3.9 33.4 - - + -
201M LEU* 5.4 1.8 - - + -
205M VAL* 4.4 19.7 - - + +
207M LYS* 4.1 41.9 + - + +
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Residues in contact with PHE 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135I THR* 4.8 11.2 - - - -
136I ALA* 4.7 3.1 - - - -
137I ALA* 3.5 38.6 - - + -
183I THR* 5.1 7.4 - - + -
114M SER* 3.5 33.2 - - - -
115M VAL* 1.3 98.7 - - - +
117M ILE* 1.3 61.8 + - - +
118M PHE* 4.2 13.9 - + + -
133M VAL 4.6 0.4 - - - -
134M CYS* 3.3 10.6 - - - -
135M LEU* 2.9 47.7 + - + +
137M ASN* 4.5 6.5 - - + -
207M LYS* 5.0 3.6 - - - -
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Residues in contact with ILE 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127I SER* 5.3 9.0 - - - -
116M PHE* 1.3 77.2 - - - +
118M PHE* 1.3 81.0 + - - +
119M PRO* 4.4 3.0 - - + +
132M VAL* 3.5 27.8 - - + -
133M VAL 3.5 7.4 - - - +
134M CYS* 4.3 3.6 - - + +
148M TRP* 3.7 22.0 - - + -
192M TYR 5.0 1.6 - - - +
194M CYS* 4.7 5.8 - - + -
207M LYS* 3.9 32.1 - - + +
208M SER 4.1 15.9 - - - +
209M PHE* 3.9 24.7 - - + -
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Residues in contact with PHE 118 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I LEU* 3.9 42.6 - - + -
125I ALA 3.4 23.3 - - - +
126I PRO* 4.4 3.1 - - + -
127I SER 5.3 1.1 - - - -
137I ALA* 3.3 42.6 - - + -
138I LEU* 4.3 4.5 - - - -
181I VAL* 5.4 3.8 - - + -
116M PHE* 4.2 18.6 - + + -
117M ILE* 1.3 82.2 - - - +
119M PRO* 1.3 69.7 - - + +
131M SER 4.2 0.5 - - - +
132M VAL* 3.3 10.0 - - - +
133M VAL* 3.0 56.2 + - + +
135M LEU* 4.5 15.3 - - + -
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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