Contacts of the strand formed by residues 163 - 166 (chain D) in PDB entry 3P1M
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 MET 163 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D THR 3.9 0.6 + - - -
69D VAL* 3.8 12.2 - - + -
70D HIS* 2.9 25.8 + - - +
89D LEU* 3.8 33.9 - - + -
119D PHE* 4.5 2.5 - - + -
120D GLU* 3.2 11.0 - - - +
122D HIS* 5.8 0.9 - - - +
123D ILE* 4.0 29.8 - - + -
156D LEU* 3.9 19.3 - - + -
160D MET* 2.9 43.7 + - + +
161D ASP 3.2 1.2 + - - -
162D ASN* 1.3 80.1 - - - +
164D THR* 1.3 61.3 + - - +
165D VAL* 3.9 19.3 - - + -
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Residues in contact with THR 164 (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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70D HIS* 3.2 26.5 - - + +
72D ILE* 3.8 36.3 - - + -
78D THR* 5.7 1.1 - - + -
120D GLU* 2.7 38.8 + - - +
162D ASN 4.3 1.7 + - - -
163D MET* 1.3 75.0 - - - +
165D VAL* 1.3 69.9 + - - +
183E THR* 3.7 13.2 - - - +
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Residues in contact with VAL 165 (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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69D VAL* 4.4 3.6 - - + -
70D HIS 2.9 11.8 + - - +
71D PHE* 3.4 36.0 - - + -
72D ILE 2.9 22.3 + - - -
89D LEU* 4.8 2.9 - - + -
117D LEU* 4.1 16.2 - - + -
118D ILE 3.2 9.4 - - - +
119D PHE* 3.7 37.9 - - + -
163D MET* 3.9 19.3 - - + -
164D THR* 1.3 81.6 - - - +
166D ARG* 1.3 59.6 + - - +
183E THR* 4.6 0.7 - - - -
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Residues in contact with ARG 166 (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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72D ILE* 3.6 26.9 - - + +
73D ASN 5.2 1.3 - - - +
117D LEU* 3.6 4.8 - - - -
118D ILE* 2.9 56.1 + - + +
145D THR* 5.6 0.8 - - - +
165D VAL* 1.3 73.7 - - - +
167D VAL* 1.3 69.7 + - - +
168D PRO* 3.4 26.5 - - - +
169D GLU 4.9 1.6 - - - +
182E LYS* 2.9 41.6 + - - +
183E THR* 3.3 29.2 + - - +
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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