Contacts of the helix formed by residues 125 - 129 (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 GLY 125 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A MET* 3.6 17.6 - - - +
123D VAL* 3.2 6.7 - - - +
124D ARG* 1.3 78.1 - - - +
126D GLY* 1.3 65.7 + - - +
127D HIS 3.7 0.3 + - - -
128D HIS 3.9 1.4 + - - -
129D HIS* 3.1 38.6 + - - +
130D SER* 3.2 15.1 + - - -
304D ASP* 3.7 1.0 + - - -
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Residues in contact with GLY 126 (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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126A ARG 4.7 0.2 - - - -
128A MET* 4.2 9.4 - - - -
124D ARG 3.4 4.2 + - - -
125D GLY* 1.3 78.8 - - - +
127D HIS* 1.3 63.7 + - - -
130D SER* 2.9 22.9 + - - -
299D TYR* 3.2 16.0 - - - +
300D PRO 4.5 0.9 - - - -
301D TYR* 4.1 28.1 - - - +
304D ASP* 4.8 1.4 + - - -
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Residues in contact with HIS 127 (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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126A ARG 3.1 27.3 + - - -
127A GLN* 3.8 17.7 + - - +
128A MET* 6.0 0.2 - - - +
144A SER* 5.7 0.2 + - - -
100B LYS* 4.3 15.0 - - + -
103B TYR* 3.3 36.8 - + - -
104B ARG* 3.5 34.2 + - + +
85D ASP* 3.4 4.0 - - - +
125D GLY 3.7 0.4 + - - -
126D GLY* 1.3 72.6 - - - +
128D HIS* 1.3 75.4 + + + +
129D HIS 3.7 0.2 - - - -
131D GLN* 3.1 27.4 + - - +
298D PRO* 4.1 13.0 - - + -
299D TYR* 2.6 32.7 + - - +
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Residues in contact with HIS 128 (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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127A GLN* 5.0 1.3 + - - -
143A ALA* 5.7 1.8 - - + -
144A SER* 3.3 29.9 + - - -
145A PRO* 3.4 27.9 - - + +
96B SER* 2.9 34.5 + - - -
100B LYS* 3.8 29.4 - - + +
104B ARG* 6.5 0.7 - - - -
85D ASP* 2.8 36.6 - - - +
86D TYR* 3.2 12.3 + + + +
125D GLY 3.9 1.4 + - - -
126D GLY 3.4 0.4 - - - -
127D HIS* 1.3 86.1 - + + +
129D HIS* 1.3 74.7 + - - +
131D GLN* 3.7 14.5 + - - -
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Residues in contact with HIS 129 (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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66A PHE* 5.7 3.4 - + - -
128A MET* 3.6 22.1 - - + +
144A SER* 5.4 0.9 - - - -
1403A COI 2.9 42.4 + - + +
83D PHE* 3.8 34.8 - + + -
85D ASP* 3.7 4.0 - - - -
86D TYR* 3.0 16.6 + + - -
123D VAL* 3.6 14.4 - - + +
125D GLY* 3.1 24.1 + - - +
128D HIS* 1.3 96.8 - - + +
130D SER* 1.3 63.8 + - - +
174D LYS* 3.1 19.7 + - - -
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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
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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