Contacts of the strand formed by residues 115 - 119 (chain A) in PDB entry 3Q29
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 SER 115 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ALA 3.7 1.4 + - - -
114A LEU* 1.3 74.7 + - - +
116A LEU* 1.3 64.1 + - - +
117A ILE* 3.6 1.9 + - - +
227A ILE* 3.6 5.5 - - - +
228A ASN 3.1 31.1 + - - +
233A TRP* 5.8 0.7 - - - -
245A VAL* 3.4 27.9 - - - +
246A THR 3.5 2.5 - - - -
248A LEU* 3.7 6.5 - - - -
321A THR* 3.5 25.6 + - - -
324A ASN* 2.8 23.8 + - - +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER* 1.3 71.8 - - - +
117A ILE* 1.3 63.3 + - - +
118A TYR* 5.1 0.7 - - + -
126A PRO* 4.3 11.7 - - + -
127A PRO 4.4 7.0 - - - +
133A ILE* 6.2 0.4 - - + -
148A LEU* 4.7 4.3 - - + -
225A MET* 3.9 37.7 - - + -
226A THR 3.8 13.2 - - - +
227A ILE* 4.4 12.6 - - + -
244A GLY 3.8 0.2 - - - +
245A VAL* 3.4 3.5 - - - -
246A THR* 2.8 62.7 + - + +
247A VAL 3.9 9.4 - - - +
248A LEU* 3.6 12.3 - - + +
249A PRO* 4.1 25.1 - - + -
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Residues in contact with ILE 117 (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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115A SER 4.0 8.1 - - - +
116A LEU* 1.3 77.9 - - - +
118A TYR* 1.3 63.6 + - - +
218A PHE* 3.6 25.0 - - + -
225A MET* 3.2 5.5 - - - +
226A THR* 2.9 46.0 + - + +
228A ASN* 3.9 31.6 - - + +
232A ALA* 5.0 0.9 - - + -
233A TRP* 4.0 26.7 - - + +
236A ILE* 3.9 18.8 - - + -
243A TYR* 3.9 9.4 - - + -
244A GLY 3.4 9.4 - - - +
245A VAL* 4.4 12.3 - - + -
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Residues in contact with TYR 118 (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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116A LEU* 5.1 1.3 - - + -
117A ILE* 1.3 75.0 - - - +
119A ASN* 1.3 62.3 + - - +
120A LYS* 3.5 34.2 - - + +
123A LEU* 3.3 29.4 - - + -
124A PRO 3.9 6.7 + - - -
126A PRO* 3.7 42.2 - - + +
218A PHE* 3.5 6.3 - - - -
224A ALA 3.3 8.7 - - - +
225A MET* 4.0 12.6 - - + -
243A TYR* 3.1 6.4 - - - +
244A GLY* 2.9 56.8 + - - -
245A VAL 4.8 0.2 - - - -
246A THR* 4.0 22.0 - - + -
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Residues in contact with ASN 119 (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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118A TYR* 1.3 70.6 - - - +
120A LYS* 1.3 60.0 + - - +
121A ASP* 3.0 23.5 + - - +
122A LEU* 3.3 34.5 + - + +
123A LEU* 2.8 30.7 + - - +
218A PHE* 3.5 14.6 + - + -
221A GLY* 4.1 16.2 - - - -
223A THR 4.4 1.4 + - - +
224A ALA* 2.9 16.3 + - - +
241A VAL* 3.8 20.7 - - - +
242A ASN 3.7 6.9 + - - +
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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