Contacts of the strand formed by residues 158 - 163 (chain I) in PDB entry 4XLN
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 TYR 158 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149I THR 3.3 10.5 - - - +
150I PRO* 3.5 26.5 - - + -
151I ASP* 3.3 13.6 - - - +
154I ARG* 4.5 4.3 + - - -
156I GLY 4.6 6.7 - - - -
157I ARG* 1.3 94.3 + - - +
159I ILE* 1.3 60.8 - - - +
176I VAL* 4.7 8.7 + - - +
310I LEU* 3.8 12.8 - - - +
313I LEU* 3.5 56.4 - - + +
314I THR* 3.7 16.4 - - + +
322I VAL* 3.8 11.2 - - + -
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Residues in contact with ILE 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147I TYR 4.2 0.2 - - - +
148I PHE* 3.6 1.4 - - - -
149I THR* 2.9 52.3 + - - +
150I PRO 4.0 0.4 - - - +
151I ASP* 3.3 31.0 - - - +
152I PRO* 4.0 9.0 - - + -
158I TYR* 1.3 73.5 - - - +
160I ALA* 1.3 65.0 + - - +
161I SER* 4.5 2.5 + - - +
173I ASP* 3.3 29.6 - - - +
174I LEU 3.2 19.1 - - - +
175I GLU* 3.6 25.6 - - + +
310I LEU* 4.1 4.3 - - - -
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Residues in contact with ALA 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147I TYR 3.3 6.5 - - - +
148I PHE* 3.5 26.9 - - + -
159I ILE* 1.3 77.7 - - - +
161I SER* 1.3 60.1 + - - +
173I ASP* 2.8 23.9 - - - +
174I LEU* 3.3 19.6 + - + +
306I THR* 4.4 9.9 - - - +
310I LEU* 3.7 28.2 - - + +
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Residues in contact with SER 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142I ARG* 5.3 5.2 - - - -
146I VAL* 3.2 8.5 - - - +
147I TYR* 2.8 40.0 + - - -
149I THR* 5.2 6.9 + - - +
159I ILE* 4.5 5.4 + - - +
160I ALA* 1.3 80.9 + - - +
162I ILE* 1.3 66.9 + - - +
163I ILE* 5.0 7.0 - - - -
171I TRP* 6.6 0.2 - - - -
172I ILE 3.7 8.5 - - - -
173I ASP* 3.0 12.9 + - - +
174I LEU 5.0 0.2 - - - +
306I THR* 4.8 0.9 + - - -
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Residues in contact with ILE 162 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145I GLY 3.8 3.6 - - - +
146I VAL* 3.6 19.5 - - + -
160I ALA* 6.2 0.2 - - + -
161I SER* 1.3 80.1 - - - +
163I ILE* 1.3 65.4 + - - +
171I TRP* 3.8 2.1 - - - +
172I ILE* 2.7 75.1 + - + +
174I LEU* 6.3 1.3 - - + -
267I TYR* 4.2 2.5 - - - +
269I LEU* 4.7 7.4 - - + -
290I LEU* 4.0 16.2 - - + -
302I VAL* 3.9 17.5 - - + -
303I PHE* 4.7 9.4 - - + -
306I THR* 3.7 30.5 - - + +
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Residues in contact with ILE 163 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141I HIS* 5.6 5.2 - - + -
142I ARG* 4.3 28.0 - - - +
144I PRO* 3.3 9.3 - - + +
145I GLY* 2.9 44.6 + - - +
147I TYR* 4.1 19.3 - - + -
161I SER* 5.0 4.3 - - - -
162I ILE* 1.3 80.5 - - - +
164I PRO* 1.3 80.6 - - + +
165I LEU 5.3 1.6 - - - +
166I PRO* 5.7 1.1 - - + -
171I TRP* 3.1 48.2 - - + +
267I TYR* 4.5 1.3 - - - -
269I LEU* 4.0 6.2 - - - +
37R T 6.2 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
------------------------------------------------------------
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