Contacts of the helix formed by residues 303 - 308 (chain D) in PDB entry 1UMD
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 GLN 303 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A LYS 5.2 2.5 + - - +
125A GLY 4.8 1.6 - - - +
126A ARG* 5.5 4.7 + - - +
339A VAL* 3.9 12.2 - - + +
340A PRO 3.0 23.6 + - - -
341A PRO* 3.6 25.6 - - + +
343A TRP* 3.8 7.7 - - - +
344A MET* 3.4 42.1 - - + +
300D PRO* 3.4 21.4 - - + +
301D TYR 3.2 0.6 - - - -
302D ALA* 1.3 83.7 + - - +
304D ASP* 1.3 65.6 + - - +
305D LYS* 3.2 3.8 - - - -
306D LEU* 2.9 21.9 + - + +
307D TYR* 3.0 10.9 + - - +
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Residues in contact with ASP 304 (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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122D GLY* 3.1 18.1 + - - -
123D VAL 3.8 1.9 + - - -
124D ARG* 2.8 43.3 + - + -
125D GLY 3.7 3.5 + - - -
126D GLY 4.8 0.2 + - - -
130D SER* 4.5 0.3 + - - -
299D TYR* 3.0 32.5 + - - -
300D PRO 3.5 11.1 + - - +
301D TYR 3.1 17.3 + - - +
302D ALA 3.4 1.6 - - - +
303D GLN* 1.3 76.0 - - - +
305D LYS* 1.3 65.3 + - + +
306D LEU 3.2 1.0 + - - -
307D TYR* 3.2 8.8 + - - +
308D LEU* 3.3 13.0 + - - +
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Residues in contact with LYS 305 (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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302D ALA 5.1 1.5 + - - +
303D GLN 3.2 1.1 - - - -
304D ASP* 1.3 81.1 - - + +
306D LEU* 1.3 68.5 + - + +
308D LEU* 3.8 9.7 - - - +
310D THR* 3.8 18.7 - - - +
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Residues in contact with LEU 306 (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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341A PRO* 3.7 34.8 - - + -
344A MET* 3.9 13.2 - - + -
363A LEU* 4.1 18.1 - - + +
366A GLU* 4.7 14.2 - - - +
367A LEU* 4.1 23.1 - - + -
295D PHE* 3.6 13.5 - - - -
303D GLN* 2.9 15.0 + - + +
305D LYS* 1.3 86.9 - - + +
307D TYR* 1.3 67.4 + - - +
308D LEU 3.4 5.2 - - - +
310D THR* 4.9 4.8 - - + +
313D ARG* 4.2 5.4 + - - -
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Residues in contact with TYR 307 (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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344A MET* 4.2 3.5 - - - -
262D ASP* 3.4 21.3 + - + -
264D PRO* 3.7 18.7 - - - +
294D GLY* 3.5 11.2 - - - -
295D PHE* 2.7 56.4 + + + -
297D THR* 3.5 23.8 + - - -
298D PRO 4.3 0.2 - - - -
299D TYR* 3.4 33.7 - + + -
300D PRO* 3.4 31.0 - - + -
303D GLN 3.0 10.8 + - - +
304D ASP 3.2 6.9 + - - +
306D LEU* 1.3 75.7 - - - +
308D LEU* 1.3 62.4 + - - +
309D PRO* 3.2 2.4 - - - +
313D ARG* 2.9 24.8 + - - -
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Residues in contact with LEU 308 (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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121D GLY 4.8 1.1 - - - -
122D GLY* 3.9 19.7 - - - -
175D ARG* 3.7 33.4 - - - +
212D THR* 3.8 19.3 - - + -
213D VAL* 4.5 4.9 - - + -
216D GLU* 4.5 5.6 - - - +
262D ASP* 3.8 26.2 - - + +
299D TYR* 3.8 15.3 - - - +
304D ASP* 3.3 9.3 + - - +
305D LYS* 3.8 7.4 - - - +
306D LEU 3.7 6.6 - - - +
307D TYR* 1.3 81.4 - - - +
309D PRO* 1.3 83.4 - - + +
310D THR* 3.2 9.9 + - - +
313D ARG* 4.2 0.2 - - - -
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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