Contacts of the strand formed by residues 120 - 126 (chain A) in PDB entry 1S9D
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 VAL 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A GLN 3.0 14.1 + - - +
87A GLY* 3.4 0.5 - - - -
88A LEU* 2.8 28.4 + - - +
118A ASP 4.4 6.1 - - - +
119A ALA* 1.3 75.2 - - - +
121A LEU* 1.3 61.2 + - - +
122A LEU 4.2 0.2 - - - -
152A ASN* 3.6 20.4 - - + +
172A TRP* 3.5 34.5 - - + -
173A LEU* 3.6 16.5 - - + +
176A GLN* 3.8 24.2 - - + +
177A LEU* 4.3 9.6 - - + -
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Residues in contact with LEU 121 (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 LEU* 3.4 26.2 - - + +
90A PHE* 4.1 7.9 - - + -
107A LEU* 3.9 28.7 - - + -
111A LEU* 4.2 8.7 - - + -
119A ALA 3.7 1.0 + - - -
120A VAL* 1.3 73.0 - - - +
122A LEU* 1.3 66.5 + - - +
123A VAL* 4.0 17.9 - - + -
145A LEU* 4.4 3.4 - - + -
148A LEU* 3.9 28.0 - - + -
151A ARG* 4.4 10.8 - - + -
152A ASN 2.9 10.5 + - - +
153A TRP* 3.0 20.7 - - + -
154A TYR 3.0 24.1 + - - -
172A TRP* 3.8 5.6 - - - -
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Residues in contact with LEU 122 (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 LEU 2.9 11.5 + - - +
89A ILE* 3.2 23.8 - - + +
90A PHE 2.8 24.9 + - - -
120A VAL 4.2 0.6 + - - -
121A LEU* 1.3 73.2 - - - +
123A VAL* 1.3 72.6 + - - +
124A PHE* 3.8 22.4 - - + -
154A TYR* 3.5 31.0 - - + +
156A GLN* 4.2 4.7 - - + -
169A GLY* 3.5 37.9 - - - +
170A LEU* 4.2 2.5 - - + +
172A TRP* 4.4 10.3 - - + -
173A LEU* 4.3 14.3 - - + +
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Residues in contact with VAL 123 (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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90A PHE* 3.3 17.3 - - + +
92A VAL* 4.4 4.5 - - + -
107A LEU* 4.9 1.3 - - + -
121A LEU* 4.0 25.6 - - + -
122A LEU* 1.3 74.5 - - - +
124A PHE* 1.3 69.9 + - - +
125A ALA 3.7 0.4 + - - +
143A LEU* 3.9 24.7 - - + -
145A LEU* 3.9 24.2 - - + -
153A TRP* 5.7 0.4 - - + -
154A TYR 2.8 14.7 + - - +
155A ILE* 3.4 21.5 - - + -
156A GLN* 2.9 29.5 + - - +
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Residues in contact with PHE 124 (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 ILE* 3.7 28.7 - - + -
89A ILE* 3.5 33.2 - - + -
90A PHE 2.9 10.2 + - - +
91A VAL* 4.3 11.2 - - + -
92A VAL* 3.1 27.4 + - - +
122A LEU* 3.8 22.8 + - + -
123A VAL* 1.3 73.4 - - - +
125A ALA* 1.3 60.5 + - - +
126A ASN* 3.1 3.6 + - - +
156A GLN* 3.4 17.3 - - + -
158A THR* 3.3 34.1 - - + +
166A LEU* 3.8 35.9 - - + -
169A GLY* 4.2 1.6 - - - -
170A LEU* 4.1 8.3 - - + -
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Residues in contact with ALA 125 (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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92A VAL* 4.0 7.0 - - - -
94A SER* 3.0 17.3 - - - +
123A VAL* 3.7 2.4 + - - -
124A PHE* 1.3 69.7 - - - +
126A ASN* 1.3 56.0 + - - +
128A GLN* 3.3 18.9 - - - +
136A ALA* 4.6 6.5 - - - -
139A ILE* 4.3 10.3 - - + -
155A ILE* 4.1 23.6 - - + -
156A GLN 2.8 13.6 + - - +
157A ALA* 4.3 6.5 - - - -
158A THR* 3.0 19.7 + - - -
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Residues in contact with ASN 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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28A ALA 2.9 24.6 + - - +
29A GLY* 3.8 3.8 + - - -
33A ILE* 5.0 1.6 - - - -
91A VAL* 4.1 9.7 - - + +
92A VAL 2.9 19.1 + - - +
94A SER* 2.8 31.5 + - - -
124A PHE* 3.1 6.5 + - + +
125A ALA* 1.3 73.0 - - - +
127A LYS* 1.3 71.3 + - - +
158A THR* 3.0 18.3 + - - +
160A ALA* 2.9 34.5 + - - +
401A GDP 3.1 26.8 + - - -
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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