Contacts of the helix formed by residues 165 - 170 (chain B) in PDB entry 1D1T
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 165 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B LYS* 4.8 0.2 - - - +
163B ALA 3.2 10.5 - - - +
164B ALA* 1.3 79.8 - - + +
166B PRO* 1.3 65.2 - - + +
167B GLU* 3.4 19.7 - - - +
168B LYS* 2.9 39.7 + - + -
169B VAL* 3.0 17.1 + - + +
335B PHE* 4.0 10.8 - - + -
336B LEU* 4.0 14.1 - - + -
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Residues in contact with PRO 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 3.8 41.1 - - + -
42B ALA* 3.8 5.3 - - + +
70B THR* 2.9 36.8 + - + +
88B LYS* 3.7 19.5 - - - +
164B ALA 3.1 5.5 - - - +
165B PRO* 1.3 83.3 - - + +
167B GLU* 1.3 66.3 + - - +
168B LYS 3.0 5.4 + - - -
170B CYS* 3.3 12.3 + - - +
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Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 3.6 15.4 - - + +
165B PRO* 3.7 10.6 - - - +
166B PRO* 1.3 85.6 - - - +
168B LYS* 1.3 90.9 + - - +
170B CYS* 3.8 3.9 - - - -
346B ILE* 3.3 18.4 - - - +
349B VAL* 4.9 17.8 - - + +
371B VAL* 3.6 24.5 - - + +
373B THR* 5.0 6.5 - - - +
101D ASN* 5.2 8.5 + - - +
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Residues in contact with LYS 168 (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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165B PRO* 2.9 26.2 + - + +
167B GLU* 1.3 112.4 + - - +
169B VAL* 1.3 58.8 + - - +
170B CYS* 2.8 10.9 + - - -
171B LEU* 3.2 15.9 + - - +
335B PHE* 4.0 16.2 - - + -
342B LEU* 3.4 15.5 - - + +
343B ASP* 2.7 41.9 + - - +
346B ILE* 4.0 11.8 - - + +
349B VAL* 5.7 1.2 - - - +
99D GLU 4.0 11.2 + - - -
100D CYS* 5.9 1.6 - - - +
101D ASN* 5.8 2.4 + - - -
104D ARG* 4.1 8.7 - - - +
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Residues in contact with VAL 169 (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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70B THR* 3.5 27.1 - - + +
90B ILE* 3.1 20.7 - - + +
160B ILE* 3.8 14.6 - - + -
164B ALA* 3.6 26.0 - - + -
165B PRO* 3.0 18.1 + - + +
168B LYS* 1.3 73.0 - - - +
170B CYS* 1.3 60.5 + - - +
171B LEU 3.1 1.1 - - - -
172B ILE* 3.2 20.2 + - + +
332B VAL* 4.5 7.2 - - + -
335B PHE* 3.5 28.9 - - + -
342B LEU* 3.9 8.1 - - - -
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Residues in contact with CYS 170 (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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42B ALA* 4.1 4.7 - - - +
44B GLY 4.2 9.9 - - - -
68B GLU* 3.0 17.0 - - - +
69B ALA* 3.8 14.8 + - - -
70B THR* 3.0 33.7 + - - +
166B PRO 3.3 10.7 + - - +
167B GLU* 3.8 17.7 - - - -
168B LYS 2.8 2.2 + - - -
169B VAL* 1.3 79.4 - - - +
171B LEU* 1.3 72.6 + - - +
172B ILE 3.0 0.7 - - - -
173B GLY* 2.9 19.8 + - - +
371B VAL* 4.1 16.2 - - - -
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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