Contacts of the strand formed by residues 121 - 128 (chain A) in PDB entry 3L6D
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 HIS 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A HIS* 4.5 11.2 + - - -
95A ARG 2.8 25.3 + - - +
96A THR* 3.4 8.6 - - - +
97A ILE 2.9 26.7 + - - +
115A VAL* 3.7 4.2 - - - +
116A ASN* 4.3 1.9 + - - -
119A GLY 4.3 9.1 + - - -
120A GLY* 1.3 81.2 + - - -
122A TYR* 1.3 61.0 + - - +
123A VAL 3.9 0.2 + - - -
146A ASP* 3.1 26.8 + - - +
148A GLU* 5.9 3.6 - - - +
149A ALA* 3.6 20.6 - - + -
152A GLN* 6.4 0.2 - - - -
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Residues in contact with TYR 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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79A THR* 6.4 0.2 - - + -
97A ILE* 3.7 11.7 - - + -
99A ASP* 2.5 46.2 + - + +
103A ASN* 5.1 1.2 + - - -
108A GLY* 3.9 18.9 + - - -
111A LEU* 3.9 23.0 - - + +
112A GLN* 3.6 33.2 + - + +
115A VAL* 3.9 32.9 - - + +
116A ASN* 4.4 5.4 + - - +
121A HIS* 1.3 73.9 - - - +
123A VAL* 1.3 61.5 + - - +
124A LYS* 4.0 21.4 + - + +
145A GLY* 3.6 4.9 - - - -
146A ASP* 2.9 28.9 + - - +
169A TRP* 4.0 18.2 - + - -
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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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96A THR* 3.8 18.8 - - + -
97A ILE 2.8 14.5 + - - +
98A VAL* 3.2 12.8 - - + -
99A ASP* 2.8 33.6 + - - +
122A TYR* 1.3 78.5 - - - +
124A LYS* 1.3 63.7 + - - +
143A HIS* 3.8 25.1 - - + -
144A THR 3.4 11.0 - - - +
146A ASP 3.8 21.3 - - - +
149A ALA* 4.1 3.1 - - + -
150A PHE* 3.8 24.5 - - + +
157A LEU* 4.7 1.6 - - + -
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Residues in contact with LYS 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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99A ASP* 3.6 10.8 + - - +
101A THR 4.4 8.1 + - - -
102A THR* 5.6 1.0 - - - +
103A ASN* 3.0 30.9 + - - +
108A GLY* 5.5 3.6 - - - -
122A TYR* 4.0 24.9 + - + +
123A VAL* 1.3 72.6 - - - +
125A GLY* 1.3 65.7 + - - +
126A MSE 4.0 18.7 - - + +
142A ILE 4.6 0.2 - - - -
143A HIS* 3.2 10.6 - - - -
144A THR* 2.9 55.7 + - + +
169A TRP* 4.1 16.6 - - + -
173A LEU* 3.5 29.5 - - + +
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Residues in contact with GLY 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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98A VAL* 4.9 0.2 - - - +
99A ASP 2.9 19.7 + - - +
100A TYR* 3.5 33.5 - - - +
123A VAL 4.0 0.6 + - - -
124A LYS* 1.3 77.4 + - - +
126A MSE 1.3 67.1 + - - +
142A ILE 3.4 6.3 - - - -
143A HIS* 3.5 14.4 - - - -
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Residues in contact with MSE 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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100A TYR* 4.0 1.7 - - - -
124A LYS* 4.0 36.3 - - + +
125A GLY* 1.3 77.6 - - - +
127A ILE* 1.3 62.2 + - - +
128A VAL* 3.8 2.1 + - - +
141A SER* 3.3 3.1 - - - -
142A ILE* 2.8 78.1 + - + +
143A HIS 4.6 0.2 - - - +
144A THR* 4.5 4.3 - - + -
172A ALA* 4.3 14.1 - - + +
173A LEU* 4.1 11.7 - - + -
176A ALA* 3.6 28.7 - - + -
180A HIS* 5.6 6.5 - - + -
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Residues in contact with ILE 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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20A MSE 4.6 15.9 - - + -
24A MSE 4.3 22.4 - - + -
100A TYR* 4.4 12.4 - - + -
125A GLY 4.2 1.0 - - - -
126A MSE 1.3 72.9 - - - +
128A VAL* 1.3 61.3 + - - +
129A ALA* 3.1 27.7 + - + +
134A VAL* 4.4 11.9 - - + -
140A HIS 4.0 9.0 - - - +
141A SER* 4.1 7.0 - - - -
160A LEU* 3.6 35.7 - - + +
161A ALA* 4.0 9.6 - - + -
180A HIS* 4.9 5.6 + - - -
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Residues in contact with VAL 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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126A MSE 4.3 7.4 - - - +
127A ILE* 1.3 69.8 - - - +
129A ALA* 1.3 62.2 + - - +
139A SER* 4.9 1.4 + - - -
140A HIS* 2.9 38.7 + - + +
142A ILE* 4.4 9.0 - - + -
179A LEU* 3.9 33.4 - - + -
180A HIS* 4.1 22.0 - - + +
183A ALA* 6.0 0.4 - - + -
214B THR* 4.2 7.4 - - + +
215B SER* 5.4 0.9 - - - -
217B PHE* 6.0 0.9 - - - -
218B PHE* 3.4 39.2 - - + +
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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