Contacts of the strand formed by residues 109 - 121 (chain A) in PDB entry 4SBV
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 LYS 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A TRP* 3.5 3.7 - - - +
108A SER* 1.3 79.0 - - - +
110A TYR* 1.3 65.1 + - - +
196A ARG* 3.9 9.4 - - + +
197A TYR 3.2 20.0 - - - +
198A PRO* 3.7 9.4 - - + -
199A PHE 4.3 0.2 - - - +
250A LEU* 4.1 0.2 - - - -
251A ILE* 2.9 33.2 + - + +
252A GLU* 2.5 40.7 - - + +
137C TYR* 3.6 35.3 - - + +
191C GLU 3.0 21.2 + - - -
192C VAL* 3.9 1.6 - - - +
193C SER* 3.1 32.6 + - - +
221C PRO 5.2 1.6 + - - -
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Residues in contact with TYR 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A MET* 4.1 4.0 - - - +
93A PRO* 3.1 38.6 - - + +
104A ALA* 6.4 0.9 - - + -
107A TRP* 6.1 0.4 - - + -
109A LYS* 1.3 80.7 - - - +
111A ALA* 1.3 77.0 + - - +
112A TRP* 3.8 24.6 + + - -
196A ARG* 3.3 9.4 - - - +
197A TYR* 2.9 61.2 + + + +
198A PRO 3.5 19.3 + - - -
199A PHE* 4.4 3.8 - - + -
219A LEU 4.8 1.2 + - - -
221A PRO* 4.0 14.7 - - - +
248A ILE* 3.2 30.5 - - + -
249A ARG 3.1 18.4 - - - +
250A LEU* 4.2 6.3 - - + -
251A ILE* 4.6 3.4 - - - +
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Residues in contact with ALA 111 (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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110A TYR* 1.3 86.5 - - - +
112A TRP* 1.3 68.0 - - - +
113A VAL* 3.5 0.6 + - - -
195A LYS 4.0 20.6 - - - +
196A ARG* 4.4 9.4 - - + +
197A TYR* 5.3 4.5 - - + +
248A ILE* 3.6 1.6 - - - +
249A ARG* 3.1 42.8 + - - +
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Residues in contact with TRP 112 (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 VAL* 3.1 21.1 + - - +
92A MET 3.6 6.5 - - - -
93A PRO* 3.5 25.4 - - + -
96A VAL* 4.0 2.9 - - + -
100A LEU* 3.7 24.0 - - + -
110A TYR* 3.8 13.8 - + - -
111A ALA* 1.3 78.1 - - - +
113A VAL* 1.3 57.7 + - - +
114A ALA 4.0 15.3 - - - +
115A ILE* 3.4 44.0 - - + -
187A LEU* 4.4 12.1 - - + -
189A THR* 2.7 30.1 + - - +
192A VAL* 6.0 1.6 - - + -
197A TYR* 5.9 0.9 - + - -
221A PRO* 3.5 25.2 - - + +
246A TYR* 3.7 14.8 - - + -
248A ILE* 3.7 25.6 - - + -
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 4.9 9.4 - - + -
111A ALA 3.5 1.4 + - - -
112A TRP* 1.3 74.3 - - - +
114A ALA* 1.3 65.0 - - + +
189A THR* 3.3 19.9 - - - +
247A THR* 2.7 35.9 + - + +
249A ARG* 4.2 25.4 - - + -
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Residues in contact with ALA 114 (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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112A TRP* 3.2 4.4 - - - -
113A VAL* 1.3 88.1 - - + +
115A ILE* 1.3 63.9 - - - +
187A LEU 6.1 0.2 - - - -
189A THR* 4.8 7.9 - - + -
245A SER 4.2 1.6 - - - +
246A TYR* 3.0 5.7 - - - +
247A THR* 2.5 45.1 + - - +
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Residues in contact with ILE 115 (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 VAL* 3.8 12.8 - - + -
96A VAL* 3.8 22.7 - - + -
112A TRP* 3.4 47.8 - - + -
114A ALA* 1.3 79.5 - - - +
116A ARG* 1.3 75.3 - - - +
117A TYR* 3.9 15.7 - - + +
186A ALA* 3.6 1.4 - - - +
187A LEU* 3.0 53.3 + - + +
189A THR* 5.9 0.7 - - - -
244A ALA* 4.9 2.9 - - + -
245A SER 3.1 8.0 + - - -
246A TYR* 3.9 7.9 - - + +
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Residues in contact with ARG 116 (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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115A ILE* 1.3 86.8 - - - +
117A TYR* 1.3 66.7 + - - +
118A THR* 4.2 3.7 + - - -
170A PHE* 2.7 50.8 - - - -
179A THR* 5.7 1.8 - - - +
184A THR* 3.5 20.3 - - - +
185A ILE 3.3 19.1 - - - +
186A ALA* 3.4 28.3 - - + +
243A TYR 3.2 2.1 - - - +
244A ALA* 3.2 3.7 - - - -
245A SER* 2.8 49.1 + - - +
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Residues in contact with TYR 117 (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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75A SER* 3.6 21.5 - - - -
89A GLU* 5.4 4.5 - - + +
90A LEU 4.3 2.6 + - - -
91A VAL* 3.2 30.6 - - + +
96A VAL* 3.5 15.9 - - + +
115A ILE* 4.2 16.8 - - + -
116A ARG* 1.3 74.4 - - - +
118A THR* 1.3 59.3 + - - +
133A MET* 4.1 2.7 - - + +
135A PHE* 4.2 19.7 - + - -
183A ILE 3.9 0.3 - - - +
184A THR* 2.8 9.2 + - - -
185A ILE* 2.7 53.9 + - + +
224A LEU* 3.6 25.7 - - + +
242A LEU* 3.8 29.8 - - + -
243A TYR 3.2 4.0 - - - -
244A ALA* 3.8 21.8 - - + -
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Residues in contact with THR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 4.2 5.2 + - - -
117A TYR* 1.3 75.2 - - - +
119A TYR* 1.3 66.5 + - - +
120A LEU* 4.6 2.9 - - + -
167A GLY* 3.9 35.7 - - - +
170A PHE* 4.0 16.0 - - + +
171A VAL* 4.8 10.8 - - + +
183A ILE 3.3 9.6 - - - +
184A THR* 2.7 24.3 + - - +
242A LEU* 3.2 5.2 - - - +
243A TYR* 2.5 44.9 + - - +
245A SER* 5.4 1.7 - - - -
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Residues in contact with TYR 119 (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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78A LEU* 3.6 24.5 - - + -
118A THR* 1.3 76.8 - - - +
120A LEU* 1.3 72.1 - - - +
121A PRO* 3.7 8.7 - - + +
131A ILE* 3.4 36.1 - - + -
133A MET* 4.7 0.2 - - + -
160A PRO 4.8 0.9 - - - -
161A VAL* 2.5 34.1 + - - -
163A GLU 3.6 22.9 - - - -
164A GLY* 3.9 8.7 - - - +
183A ILE* 3.0 30.8 + - + +
239A THR* 3.1 30.1 + - + +
240A GLY* 3.9 13.0 - - - -
241A ARG 3.1 9.9 - - - +
242A LEU* 3.8 10.5 - - + -
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Residues in contact with LEU 120 (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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118A THR* 4.6 2.7 - - + -
119A TYR* 1.3 87.2 - - - +
121A PRO* 1.3 72.9 - - + +
122A SER* 4.7 0.7 - - - -
164A GLY 3.5 19.1 - - - +
165A GLN* 4.1 11.9 - - - +
167A GLY* 4.3 4.5 - - - -
168A LEU* 4.1 32.8 - - + +
171A VAL* 3.9 26.0 - - + -
240A GLY* 3.2 2.3 - - - -
241A ARG* 2.8 31.4 + - - +
243A TYR* 3.7 28.4 - - + +
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Residues in contact with PRO 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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119A TYR* 3.7 4.9 - - + -
120A LEU* 1.3 92.9 - - + +
122A SER* 1.3 60.4 - - - +
123A CYS 4.7 4.5 - - - +
161A VAL 3.9 4.5 - - - +
162A TRP* 3.2 29.2 - - - +
163A GLU 3.4 21.8 - - - +
164A GLY* 3.8 2.0 - - - -
165A GLN* 3.7 38.4 + - + +
239A THR 3.8 6.5 - - - +
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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