Contacts of the strand formed by residues 125 - 130 (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 ILE 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A PHE* 6.5 0.2 - - + -
90A PHE* 5.8 0.2 - - - -
91A PHE* 3.2 2.6 - - - +
92A ILE* 2.9 48.5 + - + +
124A VAL* 1.3 78.7 - - - +
126A ALA* 1.3 67.0 + - - +
127A VAL* 5.8 2.7 - - + -
149A ILE* 5.2 4.0 - - + -
150A ASP 3.2 7.9 - - - +
151A VAL* 4.8 12.6 - - + -
183A LEU* 5.1 18.4 - - + -
201A VAL* 4.8 13.9 - - + -
203A VAL* 4.0 24.5 - - + -
206A VAL* 3.8 24.0 - - + -
207A LEU* 3.9 22.2 - - + -
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Residues in contact with ALA 126 (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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89A ALA* 4.6 3.4 - - + -
90A PHE* 3.1 11.4 - - - +
91A PHE* 3.7 13.5 - - + -
110A LEU* 3.7 22.7 - - + -
111A PHE* 5.9 0.4 - - + -
124A VAL* 4.1 4.2 - - + -
125A ILE* 1.3 78.0 - - - +
127A VAL* 1.3 65.8 + - - +
128A GLU 3.8 0.4 - - - -
149A ILE* 3.5 4.3 - - - +
150A ASP* 2.7 50.8 + - + +
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Residues in contact with VAL 127 (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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89A ALA* 3.2 3.8 - - - -
90A PHE* 2.7 47.3 + - + +
125A ILE* 5.8 3.1 - - + -
126A ALA* 1.3 75.5 - - - +
128A GLU* 1.3 61.4 + - - +
129A PHE* 3.7 27.6 - - + -
147A ILE* 4.4 5.6 - - + -
148A GLY 3.4 9.6 - - - +
149A ILE* 4.9 3.4 - - + -
174A VAL* 4.3 17.0 - - + -
183A LEU* 4.3 14.4 - - + -
185A VAL* 3.9 37.7 - - + -
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Residues in contact with GLU 128 (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 3.7 3.8 - - - -
89A ALA* 3.9 4.3 - - + -
108A LEU* 3.9 25.8 - - + +
126A ALA* 3.8 1.2 - - + -
127A VAL* 1.3 74.5 - - - +
129A PHE* 1.3 62.8 + - - +
130A ASP* 3.3 13.3 - - - +
146A HIS* 3.3 5.2 + - - -
147A ILE* 3.2 9.5 - - - +
148A GLY 2.8 45.8 + - - +
150A ASP* 2.5 36.3 - - - +
154A ILE* 3.9 9.2 - - - +
156A SER* 3.6 4.3 + - - -
271A MN 2.2 36.5 + - - -
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Residues in contact with PHE 129 (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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73A PHE* 4.1 17.3 - + - -
75A PHE* 3.6 29.4 - + + -
77A LEU* 5.5 0.6 - - + +
87A GLY* 3.2 24.3 - - - -
88A ILE* 2.9 26.2 + - + +
89A ALA* 4.9 0.4 - - - -
90A PHE 5.2 0.9 - - - -
108A LEU* 6.0 0.2 - - - -
127A VAL* 3.7 32.3 - - + -
128A GLU* 1.3 72.5 - - - +
130A ASP* 1.3 60.2 + - - +
131A THR* 3.9 1.2 + - - +
146A HIS 3.7 5.2 - - - -
147A ILE* 3.8 30.3 - - + -
162A TRP* 4.0 16.0 - + + -
170A LEU* 3.7 23.6 - - + -
172A VAL* 3.7 29.8 - - + -
185A VAL* 4.7 0.9 - - + -
187A ALA* 4.3 2.5 - - + -
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Residues in contact with ASP 130 (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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86A ASP 3.3 10.3 - - - +
87A GLY* 4.6 0.4 - - - -
106A GLY 5.2 1.2 - - - +
108A LEU* 5.2 7.7 - - + +
128A GLU* 3.3 20.6 - - + +
129A PHE* 1.3 72.1 - - - +
131A THR* 1.3 63.2 + - - +
132A PHE 2.8 12.0 + - - +
140A TRP* 4.9 0.9 + - - -
141A ASP* 2.9 0.2 - - - +
145A PRO* 3.6 3.3 - - - +
146A HIS* 2.9 48.2 + - - +
154A ILE* 6.1 0.5 - - - +
162A TRP* 4.0 2.8 - - - -
271A MN 2.3 28.1 + - - -
272A CA 2.4 30.4 - - - -
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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