Contacts of the strand formed by residues 87 - 93 (chain A) in PDB entry 1N3Q
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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A LEU* 5.6 1.1 - - - -
86A ASP* 1.3 82.6 - - - +
88A ILE* 1.3 60.8 + - - -
108A LEU* 3.8 11.9 - - - +
129A PHE 3.2 13.9 - - - -
131A THR* 4.6 2.7 - - - -
217A ALA* 3.3 15.4 - - - -
218A ALA 3.5 3.8 + - - -
224A GLN* 3.5 5.5 + - - -
226A HIS* 3.2 24.5 + - - -
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.6 25.4 - - + -
73A PHE* 5.8 0.9 - - + -
75A PHE* 3.5 62.6 - - + -
77A LEU* 4.5 4.7 - - + -
87A GLY* 1.3 75.9 - - - -
89A ALA* 1.3 71.6 + - - +
108A LEU* 5.1 1.7 - - - +
128A GLU* 3.7 0.5 - - - +
129A PHE* 2.9 35.9 + - + +
215A PHE* 4.4 13.9 - - + -
216A SER 3.3 10.5 - - - +
226A HIS* 4.1 16.4 - - + +
228A LEU* 4.6 5.8 - - + -
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ILE* 1.3 78.5 - - - +
90A PHE* 1.3 63.0 + - - +
91A PHE* 3.9 0.9 + - - -
108A LEU* 4.4 6.7 - - + -
110A LEU* 4.0 27.4 - - + -
126A ALA* 4.6 0.9 - - + -
127A VAL 3.2 12.8 - - - +
128A GLU* 3.9 12.6 - - + -
129A PHE* 4.9 0.7 - - - -
215A PHE* 3.1 11.7 - - - +
216A SER 2.8 37.7 + - - +
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Residues in contact with PHE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PHE* 4.7 2.9 - + - -
71A SER* 3.4 32.1 - - - -
73A PHE* 3.9 23.8 - + + -
89A ALA* 1.3 72.1 - - - +
91A PHE* 1.3 60.1 + - - +
92A ILE* 4.2 24.7 - - + -
125A ILE 5.8 0.2 - - - -
126A ALA* 3.1 3.1 - - - +
127A VAL* 2.7 52.1 + - + +
129A PHE* 5.2 1.4 - - - -
174A VAL* 4.5 17.7 - - + -
213A VAL* 4.2 24.7 - - + -
214A GLY 3.3 19.7 - - - -
215A PHE* 3.8 17.9 - + + -
231A TRP* 4.2 8.1 - - - -
233A PHE* 4.3 8.5 - + - -
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Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ARG* 3.8 32.5 - - + -
51A LEU* 3.6 27.8 - - + -
89A ALA 4.1 1.3 - - - -
90A PHE* 1.3 78.4 - - - +
92A ILE* 1.3 67.5 + - - +
93A ALA* 4.0 24.0 - - + -
97A THR* 4.3 2.5 - - + -
110A LEU* 3.6 25.4 - - + -
124A VAL* 4.1 5.4 - - + -
125A ILE 3.2 11.0 - - - +
126A ALA* 3.7 11.9 - - + -
212A ARG 5.4 0.2 - - - -
213A VAL* 3.4 5.0 - - - +
214A GLY* 3.0 42.9 + - - +
215A PHE 3.4 37.2 - - - -
216A SER* 3.9 6.3 - - - -
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 4.7 4.5 - - + -
69A PHE* 3.5 39.3 - - + -
90A PHE* 4.2 13.7 - - + -
91A PHE* 1.3 79.0 - - - +
93A ALA* 1.3 67.1 + - - +
124A VAL* 3.4 3.8 - - - +
125A ILE* 2.9 45.8 + - + +
183A LEU* 5.9 0.4 - - + -
203A VAL* 6.4 0.2 - - + -
207A LEU* 3.5 23.9 - - + +
211A VAL* 3.5 29.8 - - + -
212A ARG 3.5 6.3 - - - +
213A VAL* 4.0 14.8 - - + -
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PHE* 4.0 18.3 - - + -
92A ILE* 1.3 78.1 - - - +
94A PRO* 1.3 81.3 - - + +
97A THR* 4.1 18.8 - - + +
123A GLN 3.7 8.1 - - - +
124A VAL* 4.5 4.7 - - + -
207A LEU* 4.1 4.5 - - - -
211A VAL* 3.3 9.1 - - - +
212A ARG 2.9 28.6 + - - +
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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