Contacts of the strand formed by residues 139 - 145 (chain B) in PDB entry 4XCS
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 LEU 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B ALA* 3.8 17.5 - - + -
7B LYS 3.7 31.0 - - - +
8B ILE* 3.4 9.4 - - + +
9B GLY 2.8 29.6 + - - -
10B HIS 2.9 19.1 + - - +
12B ALA* 4.1 8.9 - - + +
13B PRO* 4.9 7.2 - - + -
116B TYR* 5.3 1.8 - - + -
131B PHE* 3.9 15.7 - - + -
132B ILE 3.4 17.7 - - - +
133B ILE* 3.8 17.9 - - + +
137B GLY 3.8 1.6 + - - -
138B ILE* 1.3 72.1 - - - +
140B ARG* 1.3 60.3 + - - +
141B GLN 3.6 17.3 - - - +
142B ILE* 3.9 12.8 - - + -
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Residues in contact with ARG 140 (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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145A ASN* 3.1 25.3 - - - +
146A ASP* 2.7 61.8 + - - +
147A LEU* 5.0 0.4 - - - +
148A PRO* 5.1 3.6 - - - +
8B ILE* 3.8 4.4 - - - +
38B TYR* 3.8 5.3 + - - +
132B ILE* 2.7 20.7 + - + +
134B ASP* 3.4 27.9 + - + +
138B ILE* 3.4 20.6 - - - +
139B LEU* 1.3 77.4 - - - +
141B GLN* 1.3 58.5 + - - +
163B PHE* 3.6 37.1 + - + -
166B THR* 4.9 2.0 + - - -
167B ASP* 2.2 37.0 + - - +
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Residues in contact with GLN 141 (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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143A THR* 4.4 5.8 + - - +
144A VAL 3.3 13.2 - - - +
145A ASN* 2.9 27.6 + - + -
151A ARG* 5.9 1.2 - - - +
8B ILE* 3.7 2.6 - - - +
130B LEU* 4.3 10.2 - - - +
131B PHE* 3.3 7.8 - - - -
132B ILE* 3.1 39.6 + - + -
139B LEU* 3.6 5.8 - - - +
140B ARG* 1.3 80.0 - - - +
142B ILE* 1.3 75.2 + - - +
143B THR* 3.3 20.7 + - - +
159B LEU* 3.3 36.0 - - - +
163B PHE* 3.7 3.5 - - + -
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Residues in contact with ILE 142 (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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1A MET* 4.3 18.4 - - + -
142A ILE* 3.7 1.6 - - + +
143A THR* 3.4 3.3 - - - -
144A VAL* 2.9 41.7 + - + +
6B ALA* 4.1 23.1 - - + +
7B LYS* 4.5 0.7 - - - -
8B ILE* 3.7 20.4 - - + +
116B TYR 5.4 0.9 - - - +
130B LEU 3.3 3.6 - - - -
131B PHE* 3.8 18.6 - - + -
139B LEU* 3.9 21.5 - - + -
141B GLN* 1.3 80.2 - - - +
143B THR* 1.3 63.3 + - - +
144B VAL* 3.6 27.6 - - + +
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Residues in contact with THR 143 (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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141A GLN* 3.7 19.5 - - + +
142A ILE 3.3 2.9 - - - -
143A THR* 3.0 32.7 - - + +
128B ARG 3.7 0.7 - - - +
129B GLY* 3.2 5.2 - - - -
130B LEU* 2.8 53.7 + - + +
131B PHE* 5.2 0.2 - - - -
141B GLN* 3.3 17.1 + - - +
142B ILE* 1.3 70.0 - - - +
144B VAL* 1.3 67.0 + - - +
145B ASN* 4.2 10.5 - - - +
151B ARG* 6.2 2.9 - - - -
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Residues in contact with VAL 144 (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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0A HIS* 4.3 4.7 - - - +
1A MET* 3.9 19.3 - - + -
8A ILE* 3.4 19.6 - - + +
141A GLN* 3.2 2.3 - - - +
142A ILE* 2.9 36.5 + - + +
116B TYR 5.4 0.4 - - - +
118B VAL* 3.9 25.6 - - + -
127B PHE* 3.6 30.7 - - + -
128B ARG 3.3 5.2 - - - +
131B PHE* 4.9 0.2 - - + -
142B ILE* 3.6 21.3 - - + -
143B THR* 1.3 79.1 - - - +
145B ASN* 1.3 65.0 + - - +
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Residues in contact with ASN 145 (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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8A ILE* 4.0 8.1 - - - -
140A ARG 3.1 17.0 - - - +
141A GLN* 3.1 29.6 + - + +
159A LEU* 5.1 0.6 - - - +
163A PHE* 4.1 1.8 - - + -
127B PHE* 3.6 5.6 - - - +
128B ARG* 3.0 44.4 + - - +
143B THR* 4.2 9.0 - - - +
144B VAL* 1.3 76.8 - - - +
146B ASP* 1.3 61.2 + - - +
147B LEU* 3.0 36.0 + - - +
151B ARG* 5.4 3.7 + - - +
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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