Contacts of the strand formed by residues 195 - 200 (chain I) 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 ILE 195 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154I TRP* 3.6 6.7 - - - -
155I ASN* 2.8 54.4 + - - +
193I THR* 5.6 3.1 - - - +
194I TYR* 1.3 76.4 - - - +
196I CYS* 1.3 60.3 + - - +
197I ASN* 3.7 7.9 + - - +
208I ASP* 3.6 32.3 - - + +
209I LYS 2.9 28.5 - - - +
210I LYS* 4.5 5.4 - - + +
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Residues in contact with CYS 196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121I VAL* 3.8 13.7 - - - -
140I CYS* 2.0 51.3 - - + -
152I VAL* 4.6 6.1 - - + -
153I SER 3.4 6.5 - - - +
154I TRP* 3.6 25.5 - - + -
195I ILE* 1.3 70.1 - - - +
197I ASN* 1.3 60.7 + - - +
198I VAL* 4.4 6.7 - - - -
207I VAL 3.6 3.1 - - - +
208I ASP* 3.6 3.6 - - - -
209I LYS* 3.1 29.6 + - - -
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Residues in contact with ASN 197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151I THR* 3.1 7.6 - - - +
152I VAL* 3.3 0.6 - - - -
153I SER* 2.6 45.7 + - - +
155I ASN 3.6 2.1 + - - -
156I SER* 2.4 46.2 + - - +
195I ILE* 3.7 18.1 + - - +
196I CYS* 1.3 75.6 - - - +
198I VAL* 1.3 63.0 + - - +
199I ASN* 5.2 0.5 - - - +
206I LYS* 6.2 2.9 - - - -
207I VAL 3.8 4.3 - - - -
208I ASP* 3.0 28.8 + - - +
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Residues in contact with VAL 198 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I PRO* 4.3 18.4 - - + -
121I VAL* 3.5 37.5 - - + -
142I VAL* 3.9 18.4 - - + -
150I VAL* 4.2 18.6 - - + -
151I THR 3.2 3.4 - - - -
152I VAL* 4.5 8.5 - - + -
196I CYS* 4.4 9.4 - - - -
197I ASN* 1.3 75.3 - - - +
199I ASN* 1.3 68.0 + - - +
200I HIS 4.6 0.7 - - - +
205I THR* 5.4 0.9 - - + +
206I LYS* 3.6 7.1 - - - +
207I VAL* 2.9 41.6 + - + +
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Residues in contact with ASN 199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149I PRO 4.7 0.2 - - - +
150I VAL* 3.8 2.1 - - - -
151I THR* 2.7 50.6 + - + +
197I ASN 5.2 0.4 - - - +
198I VAL* 1.3 77.5 - - - +
200I HIS* 1.3 60.1 + - - +
201I LYS* 3.8 19.1 + - - +
205I THR 3.7 2.8 - - - +
206I LYS* 3.8 28.3 - - + +
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Residues in contact with HIS 200 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I LYS 2.9 26.4 + - - -
119I PRO* 3.5 26.4 - - + +
145I TYR* 4.2 3.1 - - + -
146I PHE 3.7 13.9 - - - -
147I PRO 2.9 20.8 + - - -
149I PRO 3.3 22.7 - - - -
150I VAL* 3.8 14.8 - - + -
198I VAL* 4.2 1.0 - - + +
199I ASN* 1.3 71.3 - - - +
201I LYS* 1.3 63.9 + - - +
202I PRO* 3.5 18.5 - - + +
203I SER* 2.9 26.3 + - - +
204I ASN* 3.1 16.2 + - - -
205I THR 2.9 20.7 + - - +
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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
------------------------------------------------------------
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