Contacts of the strand formed by residues 120 - 124 (chain L) in PDB entry 4WEB
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 THR 120 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140H SER* 5.8 4.0 - - - +
142H THR* 5.3 6.5 - - - +
187H THR* 6.1 1.8 - - + +
118L ALA 3.6 2.2 + - - -
119L PRO* 1.3 72.7 - - - +
121L VAL* 1.3 66.2 + - - +
122L SER* 4.6 8.3 + - - +
141L PHE 3.3 3.5 - - - +
142L LEU* 3.5 0.3 - - - -
143L ASN* 2.9 50.4 + - + +
144L ASN* 5.5 2.6 - - - +
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Residues in contact with VAL 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119L PRO* 3.8 12.3 + - + +
120L THR* 1.3 80.0 - - - +
122L SER* 1.3 68.5 + - - +
140L CYS* 3.6 27.8 - - - -
141L PHE 3.2 4.0 - - - +
142L LEU* 4.3 7.4 - - + -
200L CYS* 4.2 3.6 - - - +
202L ALA* 4.0 22.7 - - + -
211L ILE* 3.6 27.6 - - + +
213L LYS* 3.2 46.0 - - + +
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Residues in contact with SER 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H THR* 3.7 23.1 + - - +
120L THR* 4.6 7.1 + - - +
121L VAL* 1.3 82.0 + - - +
123L ILE* 1.3 61.5 + - - +
124L PHE* 3.6 26.2 - - - -
139L VAL 3.7 0.9 - - - +
140L CYS* 3.3 4.0 - - - -
141L PHE* 2.8 40.3 + - - +
143L ASN* 5.4 1.7 + - - -
213L LYS* 4.6 1.6 - - - +
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Residues in contact with ILE 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131H PRO* 4.9 1.0 - - - +
132H VAL* 3.7 20.4 + - + +
122L SER* 1.3 74.3 - - - +
124L PHE* 1.3 70.1 + - - +
125L PRO 4.3 0.2 - - - -
138L VAL* 4.3 5.8 - - + -
139L VAL 3.5 6.3 - - - +
140L CYS* 4.4 0.4 - - - +
154L TRP* 4.0 16.2 - - + -
198L TYR 3.8 17.7 - - - +
200L CYS* 4.0 16.2 - - - +
213L LYS* 3.4 41.4 - - + +
214L SER 3.9 17.3 - - - +
215L PHE* 3.8 23.1 - - + -
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Residues in contact with PHE 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H LEU* 3.5 40.6 - - + -
130H ALA 3.2 21.3 - - - +
131H PRO* 3.7 15.5 - - + -
142H THR* 3.0 35.2 - - + -
143H LEU 4.1 5.4 - - - -
144H GLY 4.1 1.1 - - - -
122L SER* 3.6 23.8 - - - -
123L ILE* 1.3 75.2 - - - +
125L PRO* 1.3 68.3 - - + +
138L VAL* 3.4 7.4 - - - +
139L VAL* 2.6 48.7 + - + +
141L PHE* 3.3 33.9 - + - -
215L PHE* 4.7 0.2 - - - -
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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