Contacts of the strand formed by residues 201 - 204 (chain D) in PDB entry 2J2M
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 201 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D TRP* 6.0 0.4 - - - -
127D VAL 6.4 0.2 - - - -
197D SER* 4.4 17.5 - - - -
199D HIS* 3.7 27.4 - + + -
200D SER* 1.3 78.3 - - - +
202D LYS* 1.3 65.0 + - - +
203D TRP* 5.0 3.1 - - + +
212D TYR* 3.3 6.9 - - - -
213D ILE* 2.7 51.3 + - + -
215D LEU* 5.9 2.9 - - + -
317D PRO* 3.4 32.3 - - + -
318D GLY* 5.6 0.4 - - - -
320D LEU* 4.2 17.9 - - + -
324D MET* 6.2 0.7 - - + -
325D LEU 3.8 12.6 - - - +
326D PRO* 4.3 7.4 - - + -
327D SER* 4.1 5.6 - - - +
332D LEU* 3.8 28.3 - - + -
335D ARG* 5.4 0.4 - - - -
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Residues in contact with LYS 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A HIS* 5.0 2.2 + - - -
201D PHE* 1.3 75.8 - - - +
203D TRP* 1.3 70.8 + - - +
204D VAL* 4.2 1.5 + - + -
210D THR* 4.0 14.8 - - - +
211D VAL 3.4 3.8 - - - -
212D TYR* 3.5 36.2 + - + -
267D PRO* 6.2 1.3 - - - -
324D MET* 3.4 0.5 - - - -
325D LEU* 2.8 52.0 + - + +
326D PRO 3.7 17.2 + - - +
327D SER* 4.3 0.6 - - - +
328D GLU* 3.4 25.7 + - - -
403D GLN* 2.7 47.9 + - + +
404D PRO* 4.7 6.5 + - - +
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Residues in contact with TRP 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D MET* 4.0 26.9 - - + -
75D TYR* 3.3 30.8 - - + +
76D THR* 3.7 21.8 - - + -
81D LEU* 4.2 21.3 - - + -
124D TRP* 5.3 2.0 - + - -
201D PHE* 4.1 3.4 + - + +
202D LYS* 1.3 83.1 - - - +
204D VAL* 1.3 58.0 + - - +
209D ASN 3.7 0.2 - - - +
210D THR* 3.1 2.6 - - - -
211D VAL* 2.9 32.6 + - + -
213D ILE* 3.6 45.8 - - + +
215D LEU* 4.1 17.9 - - + +
260D LEU* 6.2 1.1 - - + -
262D VAL* 3.8 26.2 - - + -
294D VAL* 5.0 4.5 - - + -
323D GLY 3.3 2.0 - - - -
324D MET* 3.7 33.7 - - + +
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Residues in contact with VAL 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D TYR 3.8 2.9 - - - -
76D THR* 3.4 0.7 - - - -
77D LYS* 3.0 24.2 + - - +
202D LYS* 4.8 2.9 - - + +
203D TRP* 1.3 78.7 - - - +
205D ASN* 1.3 70.2 + - - +
208D GLY* 4.3 9.9 - - - +
209D ASN 3.4 7.6 - - - +
210D THR* 3.7 17.9 - - + +
323D GLY* 2.9 25.1 + - - +
325D LEU* 4.1 25.4 - - + -
401D ASP* 3.4 38.4 - - - +
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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