Contacts of the strand formed by residues 128 - 133 (chain B) in PDB entry 4X61
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 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ALA* 3.1 19.9 - - - +
97B ALA* 3.4 28.7 - - + +
98B SER 3.0 10.8 + - - +
101B GLY* 3.5 31.0 - - - +
102B ALA 3.6 13.9 - - - +
103B VAL* 3.8 17.0 - - + -
124B HIS* 3.7 25.4 - - + -
127B ILE* 1.3 69.4 - - - +
129B SER* 1.3 58.1 - - - +
130B THR 4.2 1.3 - - - +
142B SER* 4.1 9.2 - - - -
143B GLY 3.9 9.4 - - - +
144B SER* 3.9 4.3 - - - -
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ARG* 5.9 2.0 - - - -
84B ALA* 3.9 13.8 - - - +
85B ASP* 3.6 15.7 - - - +
127B ILE* 3.3 11.2 + - - -
128B VAL* 1.3 73.9 - - - +
130B THR* 1.3 60.4 + - - +
143B GLY 3.0 9.7 + - - -
144B SER* 3.9 5.5 - - - -
145B LYS* 4.2 12.5 + - - +
169B GLN* 6.2 0.9 - - - -
170B VAL 2.8 27.4 + - - -
171B THR* 4.5 7.9 - - - +
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Residues in contact with THR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ASP* 3.6 12.9 + - - +
97B ALA* 4.5 1.1 - - - -
128B VAL* 3.6 2.4 - - - +
129B SER* 1.3 79.7 - - - +
131B VAL* 1.3 66.4 + - - +
142B SER* 3.3 3.8 - - - -
143B GLY* 2.8 51.8 + - - +
170B VAL* 4.1 1.6 - - + +
171B THR 3.5 23.1 - - - +
172B CYS* 3.6 7.8 - - - +
173B VAL* 3.1 39.7 + - + +
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ARG* 5.6 1.9 + - - -
85B ASP* 3.1 14.4 + - - +
86B LEU* 3.9 37.1 - - - +
87B THR* 4.4 7.9 - - + +
95B LEU* 4.1 28.7 - - + +
96B VAL 4.9 0.2 - - - -
97B ALA* 3.9 20.9 - - + +
103B VAL* 4.4 10.1 - - + -
130B THR* 1.3 83.4 + - - +
132B SER* 1.3 64.2 + - - +
141B VAL 3.5 6.1 - - - +
142B SER* 3.8 18.8 - - - -
173B VAL* 4.2 2.1 - - - +
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Residues in contact with SER 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B THR* 4.6 4.9 - - - -
95B LEU* 4.9 0.2 - - - -
131B VAL* 1.3 76.1 - - - +
133B VAL* 1.3 65.2 + - - +
140B ALA* 3.4 5.1 - - - +
141B VAL* 2.9 41.9 + - - +
173B VAL 3.4 17.2 + - - -
174B ALA* 3.6 4.2 - - - -
175B ALA* 3.0 31.1 + - - +
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B THR* 3.3 29.3 - - + +
88B TRP 3.4 17.5 - - - +
89B VAL* 3.8 17.0 - - + -
90B GLY 5.7 0.4 - - - +
95B LEU* 4.3 4.0 - - + -
132B SER* 1.3 75.7 + - - +
134B LEU* 1.3 74.3 + - - +
137B GLY* 4.0 16.4 - - - +
139B GLN 3.6 12.1 - - - +
140B ALA* 4.2 1.1 - - - -
154B LEU* 4.1 13.7 - - + -
175B ALA* 3.3 12.5 - - - +
176B SER 5.4 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