Contacts of the helix formed by residues 100 - 105 (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 LYS 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B PHE* 6.0 0.2 - - - -
127B HIS* 4.4 20.9 - - + -
128B HIS* 3.9 21.8 - - + -
131B GLN* 4.1 28.4 + - - +
298B PRO* 3.9 32.8 - - + +
299B TYR 5.6 0.2 - - - +
95D VAL* 2.8 31.2 + - - +
96D SER* 4.0 11.4 + - - +
97D GLN 3.8 2.2 + - - -
98D VAL 3.3 0.4 - - - -
99D ALA* 1.3 78.5 - - + +
101D LEU* 1.3 59.9 + - - +
102D ARG 3.5 1.8 - - - -
103D TYR* 3.3 6.5 + - - -
104D ARG* 2.8 37.4 + - + +
140D THR* 4.3 13.5 - - - +
141D ALA 4.9 2.0 + - - +
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Residues in contact with LEU 101 (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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140C PHE* 3.6 34.1 - - + -
141C THR* 5.3 0.9 - - - -
68D LEU* 3.9 20.4 - - + -
72D ALA* 4.2 3.1 - - + -
97D GLN 3.2 18.4 + - - +
98D VAL 3.5 9.3 + - - +
99D ALA 3.6 0.2 - - - -
100D LYS* 1.3 74.4 - - - +
102D ARG* 1.3 62.9 + - - +
104D ARG* 3.6 19.0 - - - +
105D SER* 2.8 34.7 + - - +
109D PHE* 3.6 29.6 - - + +
110D THR 3.7 26.9 - - - +
111D ALA* 4.8 2.9 - - + -
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Residues in contact with ARG 102 (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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347C ASP* 3.2 27.1 + - + +
348C VAL 4.4 4.9 - - - +
349C PHE* 3.5 21.2 - - - +
350C ALA* 3.6 34.3 - - - +
98D VAL 5.0 1.0 + - - -
99D ALA 5.0 2.1 + - - +
100D LYS 3.5 0.4 - - - -
101D LEU* 1.3 79.5 - - - +
103D TYR* 1.3 61.9 + - - +
106D GLY 3.3 1.0 + - - -
107D GLY* 2.8 41.2 + - - -
109D PHE 3.3 15.8 + - - +
110D THR* 3.4 36.3 - - - +
111D ALA* 5.3 1.7 - - - +
165D GLU* 4.1 21.4 + - - +
166D ASP* 3.8 9.9 + - - +
167D PRO* 6.0 1.8 - - - +
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Residues in contact with TYR 103 (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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127B HIS* 3.4 34.1 - + - -
297B THR* 4.0 0.9 + - - -
298B PRO* 3.4 41.4 + - + -
300B PRO* 3.6 17.4 - - + +
126C ARG* 3.0 50.2 + - + +
344C MET* 2.7 35.8 + - - +
346C GLU 3.2 28.3 - - - -
347C ASP* 3.1 12.5 + - - +
348C VAL* 3.7 24.2 + - + +
99D ALA 5.3 2.2 + - - +
100D LYS* 3.3 9.0 + - - +
101D LEU 3.3 0.2 - - - -
102D ARG* 1.3 77.2 - - - +
104D ARG* 1.3 61.7 + - - +
106D GLY 3.1 3.5 + - - -
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Residues in contact with ARG 104 (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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127B HIS* 3.4 30.0 + - + +
123C ASN* 3.6 15.2 - - - +
126C ARG* 4.2 3.9 - - - +
127C GLN* 3.4 30.7 + - - +
140C PHE* 3.3 17.0 - - - -
141C THR* 3.1 43.4 + - + +
142C VAL 3.5 4.6 + - - -
143C ALA* 3.9 10.9 - - - +
96D SER 3.5 14.5 + - - -
97D GLN* 2.8 50.8 + - - +
100D LYS* 2.8 23.2 + - - +
101D LEU* 3.6 21.7 - - - +
103D TYR* 1.3 73.1 - - - +
105D SER* 1.3 59.6 + - - +
106D GLY 3.3 0.9 - - - -
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Residues in contact with SER 105 (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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122C PRO 3.6 0.2 - - - +
123C ASN* 3.4 12.8 - - - -
141C THR* 3.2 22.0 - - - -
101D LEU* 2.8 22.9 + - - -
102D ARG 3.4 4.0 + - - -
103D TYR 3.2 0.2 - - - -
104D ARG* 1.3 76.7 - - - +
106D GLY* 1.3 60.9 + - - +
108D GLN* 3.0 28.9 + - - +
109D PHE* 3.0 38.5 + - - -
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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