Contacts of the strand formed by residues 114 - 118 (chain I) in PDB entry 5DST
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 VAL 114 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112I ASP 5.4 0.2 - - - +
113I LYS* 1.3 75.8 - - - +
115I VAL* 1.3 62.3 + - - +
135I LYS* 4.2 22.0 - - - -
136I LYS* 3.4 14.1 - - + +
138I PHE* 3.9 31.0 - - + -
176I VAL* 4.7 10.5 - - + -
178I LYS 4.9 1.1 - - - +
179I VAL* 3.4 19.1 - - + +
180I ASP* 3.0 40.3 + - - +
181I ILE 3.3 7.3 + - - -
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Residues in contact with VAL 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110I PHE* 4.0 19.3 - - + -
113I LYS* 4.3 2.9 - - + +
114I VAL* 1.3 81.4 - - - +
116I LEU* 1.3 59.4 + - - +
117I ASP 4.1 0.2 - - - -
129I ALA* 4.2 6.7 - - + -
134I ALA* 3.8 25.1 - - + -
136I LYS 3.0 8.2 + - - +
137I VAL* 3.3 10.3 - - + +
138I PHE* 2.7 36.6 + - - +
179I VAL* 4.2 2.7 - - - -
181I ILE* 3.3 20.4 - - + +
183I ILE* 3.9 39.3 - - + -
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Residues in contact with LEU 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I VAL* 1.3 74.8 - - - +
117I ASP* 1.3 60.8 + - - +
118I VAL* 3.7 24.0 + - + -
138I PHE* 3.3 24.9 - - + +
140I ILE* 3.8 26.7 - - + -
174I LEU* 4.2 9.9 - - + -
179I VAL* 3.8 16.3 - - + +
181I ILE 2.9 10.7 + - - +
182I ILE* 3.4 15.4 - - + +
183I ILE* 2.9 28.1 + - - +
203I ALA* 4.1 2.9 - - + -
207I TRP* 3.7 35.0 - - + -
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Residues in contact with ASP 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I VAL* 4.1 1.6 - - - +
116I LEU* 1.3 72.3 - - - +
118I VAL* 1.3 71.4 + - - +
119I GLY 3.6 3.1 + - - +
120I SER* 3.5 24.8 - - - +
123I GLY 4.9 0.2 - - - -
125I LEU* 3.3 21.6 - - - +
126I SER* 2.8 42.1 + - - +
137I VAL* 4.8 1.0 - - + +
138I PHE 2.8 11.7 + - - +
139I GLY* 3.4 3.7 - - - -
140I ILE 3.0 26.5 + - - +
183I ILE* 3.4 19.1 - - + +
184I SER* 4.4 0.5 - - - -
401I SAH 4.2 2.9 + - - -
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Residues in contact with VAL 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I LEU* 3.7 29.6 - - + -
117I ASP* 1.3 70.5 + - - +
119I GLY* 1.3 64.9 + - - +
140I ILE* 4.5 0.7 - - - -
169I VAL* 4.2 10.3 - - + -
182I ILE* 4.0 16.2 - - + -
183I ILE 3.0 7.5 + - - -
184I SER* 2.9 33.4 + - - +
185I GLU 4.6 1.6 + - - +
196I MET* 3.3 8.9 - - + +
199I THR* 3.9 28.9 - - + +
200I VAL* 4.0 20.0 - - + -
203I ALA* 3.9 13.7 - - + -
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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
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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