Contacts of the helix formed by residues 125 - 131 (chain B) in PDB entry 3QLD
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 PRO 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123B GLY 4.3 3.8 - - - +
124B GLN* 1.3 83.3 - - + +
126B LEU* 1.3 67.6 + - - +
127B VAL* 4.3 7.4 - - + -
128B GLY* 3.1 15.9 + - - +
129B LEU* 3.1 13.0 + - - +
351B GLN* 3.5 42.6 - - + +
352B CYS 3.6 7.9 - - - +
353B ALA* 4.1 2.9 - - + +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B TRP* 3.7 39.7 - - + +
116B ASP* 4.0 15.5 - - - +
119B ALA* 3.8 15.2 - - + +
124B GLN 3.1 3.2 + - - -
125B PRO* 1.3 72.0 - - - +
127B VAL* 1.3 63.8 + - - +
129B LEU* 3.2 7.3 + - + +
130B LEU* 3.1 38.0 + - + +
276B PHE* 4.1 10.8 - - + -
307B HIS* 3.9 25.1 - - + +
310B ILE* 3.7 24.2 - - + -
352B CYS* 3.1 16.6 + - - +
354B GLY* 4.3 1.3 - - - +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PRO* 4.3 4.9 - - + -
126B LEU* 1.3 79.5 - - - +
128B GLY* 1.3 61.9 + - - +
130B LEU* 3.4 4.0 + - + +
131B GLY 3.2 5.0 + - - -
132B GLY* 2.9 41.7 + - - +
134B ARG 5.1 0.7 - - - +
310B ILE* 3.8 24.4 - - + +
313B ALA* 3.5 32.3 - - + -
314B LEU* 6.1 0.2 - - + -
349B VAL* 3.9 6.7 - - + -
350B PRO 3.6 16.1 + - - +
351B GLN* 3.5 35.9 - - - +
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PRO* 3.1 13.4 + - - +
127B VAL* 1.3 81.6 - - - +
129B LEU* 1.3 64.8 + - - +
131B GLY* 3.1 13.3 + - - -
132B GLY 4.8 4.9 - - - -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B TRP* 4.3 23.9 - - + -
118B TYR* 4.0 18.8 - - + +
119B ALA* 3.9 27.4 - - + +
124B GLN* 3.4 50.5 - - + +
125B PRO 3.1 11.5 + - - +
126B LEU* 3.5 9.2 - - + +
128B GLY* 1.3 76.4 - - - +
130B LEU* 1.3 61.4 + - - +
131B GLY 3.5 0.5 + - - -
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B TRP* 3.9 38.1 - - + -
126B LEU* 3.1 22.9 + - + +
127B VAL* 3.8 5.6 - - + +
128B GLY 3.2 0.4 - - - -
129B LEU* 1.3 76.8 - - - +
131B GLY* 1.3 59.9 + - - +
276B PHE* 3.6 45.3 - - + -
280B LEU* 3.6 27.6 - - + +
310B ILE* 3.9 20.6 - - + -
314B LEU* 3.6 25.5 - - + +
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Residues in contact with GLY 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B VAL 3.2 0.2 + - - -
128B GLY 3.1 14.7 + - - -
129B LEU 3.3 1.0 + - - -
130B LEU* 1.3 80.1 - - - +
132B GLY* 1.3 61.5 + - - +
133B GLY* 3.5 3.3 + - - -
314B LEU* 4.1 2.5 - - - -
315B PRO* 3.5 20.6 - - - +
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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