Contacts of the strand formed by residues 173 - 178 (chain E) in PDB entry 3N1Q
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 TRP 173 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E PHE* 3.7 27.8 - + + +
49E VAL 3.3 6.1 - - - -
50E PRO* 3.3 24.7 + - + -
52E VAL 2.8 19.9 + - - -
53E PRO* 5.0 1.1 - - + -
54E GLU* 3.3 53.8 - - + -
59E ALA* 3.6 22.9 - - + -
60E SER* 3.3 5.8 - - - +
171E PHE* 3.1 2.0 + - - +
172E ASP* 1.3 80.8 - - - +
174E VAL* 1.3 64.1 + - - +
175E TYR* 3.5 35.4 - + + -
183E HIS* 3.7 13.6 - + - +
184E VAL* 3.5 3.5 - - - +
185E SER* 2.9 43.0 + - - +
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Residues in contact with VAL 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E LEU* 4.3 4.7 - - + +
47E GLN 4.0 0.6 - - - +
48E PHE* 3.0 6.7 - - - +
49E VAL 2.8 33.1 + - - +
163E ALA* 3.8 24.5 - - + +
166E ALA* 3.8 13.2 - - + -
167E VAL* 3.9 23.1 - - + -
171E PHE* 3.9 14.4 - - + +
173E TRP* 1.3 80.8 - - - +
175E TYR* 1.3 63.8 + - - +
182E VAL* 3.8 22.4 - - + -
183E HIS 3.4 2.7 - - - -
184E VAL* 3.8 18.8 - - + -
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Residues in contact with TYR 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E LYS* 3.4 54.2 + - - +
47E GLN 3.6 9.4 - - - -
48E PHE* 3.6 19.7 - + + -
173E TRP* 3.5 35.4 - + + -
174E VAL* 1.3 76.2 - - - +
176E TYR* 1.3 57.5 + - - +
177E GLU* 2.6 57.6 + - + -
182E VAL* 4.0 3.1 - - - -
183E HIS* 2.8 39.1 + + + +
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Residues in contact with TYR 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E LEU* 3.7 25.4 - - + +
44E LEU 3.7 17.3 - - - +
45E TYR* 3.6 26.4 - + + -
46E LYS* 3.1 18.7 + - - +
47E GLN 3.0 12.4 + - - +
156E ARG* 3.5 10.4 + - - +
159E TYR* 3.2 31.5 - - + +
160E GLY* 3.5 29.0 + - - -
163E ALA* 4.7 4.5 - - + -
174E VAL* 5.1 1.0 - - - +
175E TYR* 1.3 68.9 - - - +
177E GLU* 1.3 66.6 + - - +
178E SER 3.2 22.9 - - - -
179E ARG* 3.9 11.0 + - + +
181E HIS 4.2 3.1 - - - -
182E VAL* 4.3 10.2 - - + +
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Residues in contact with GLU 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E TYR* 3.8 0.7 - - - -
46E LYS* 2.9 33.1 + - - +
175E TYR* 2.6 43.1 + - + +
176E TYR* 1.3 74.0 - - - +
178E SER* 1.3 60.0 + - - +
181E HIS* 3.7 21.7 + - + +
183E HIS* 3.4 12.6 - - + +
190E ZN 3.1 26.0 - - - -
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Residues in contact with SER 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E TYR* 3.7 7.0 - - - -
46E LYS* 5.2 0.2 - - - +
176E TYR* 3.2 10.7 - - - -
177E GLU* 1.3 80.4 - - - +
179E ARG* 1.3 61.9 + - - +
180E ASN* 2.9 14.9 + - - +
181E HIS* 2.6 49.4 + - - +
922F GLU* 2.8 37.7 + - - -
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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