Contacts of the strand formed by residues 113 - 118 (chain A) in PDB entry 5IVH
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 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLY* 3.3 33.9 - - - +
61A ILE 3.2 6.1 - - - +
62A PRO* 3.5 30.8 - - + +
63A TYR* 3.6 7.0 - - - -
66A PRO* 4.6 6.0 - - + +
86A ARG* 5.0 5.4 + - - -
92A LYS* 3.3 42.5 + - + +
110A ASP* 2.6 47.5 + - - -
111A CYS* 2.9 18.6 + - - +
112A LEU* 1.3 78.7 - - - +
114A LEU* 1.3 62.9 + - - +
143A ASN* 3.7 5.8 + - - +
164A GLN* 3.0 33.7 + - - +
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Residues in contact with LEU 114 (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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60A GLY 3.6 2.8 + - - -
61A ILE* 2.9 46.6 + - + +
63A TYR* 3.9 20.0 - - + -
113A TYR* 1.3 75.2 - - - +
115A SER* 1.3 62.7 + - - +
116A VAL* 3.7 27.6 - - + -
143A ASN* 3.9 1.8 - - - +
161A ILE* 4.1 6.3 - - + -
162A ASN 3.4 11.2 - - - +
163A ILE* 4.1 11.7 - - + -
194A ALA* 4.1 17.7 - - + +
197A TRP* 3.7 35.7 - - + -
198A ILE* 4.3 7.0 - - + -
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Residues in contact with SER 115 (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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58A PHE 3.1 10.1 - - - -
59A GLU* 3.4 24.8 + - - +
60A GLY 3.9 1.9 + - - -
114A LEU* 1.3 72.7 - - - +
116A VAL* 1.3 64.2 + - - +
117A TYR* 3.2 29.1 + - - -
143A ASN* 3.6 15.2 + - - -
160A LEU 3.9 0.5 - - - +
161A ILE* 3.1 7.4 - - - +
162A ASN* 3.0 34.9 + - - -
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Residues in contact with VAL 116 (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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56A TYR 3.7 0.9 - - - +
57A SER* 3.7 1.4 - - - -
58A PHE* 2.7 46.6 + - + +
61A ILE* 4.1 13.5 - - + -
114A LEU* 3.7 23.1 - - + -
115A SER* 1.3 76.9 - - - +
117A TYR* 1.3 67.9 + - - +
118A THR* 5.6 1.1 - - + -
159A VAL* 4.0 20.4 - - + -
160A LEU 3.6 2.2 - - - -
161A ILE* 4.0 13.2 - - + -
197A TRP* 4.2 10.3 - - + -
205A PHE* 3.8 32.5 - - + -
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Residues in contact with TYR 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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55A TYR* 3.7 17.5 - + + -
56A TYR 3.3 6.3 - - - +
57A SER* 3.2 26.9 - - - -
59A GLU* 3.9 5.1 + - + -
115A SER* 3.2 35.6 + - - -
116A VAL* 1.3 80.9 - - - +
118A THR* 1.3 66.7 + - - +
143A ASN 3.9 7.4 + - - -
145A ARG* 3.6 31.6 - - + +
148A TYR 4.9 1.4 + - - -
150A PRO* 3.5 31.2 - - + -
154A ILE* 4.2 6.4 - - + +
158A VAL 4.2 0.2 - - - +
159A VAL* 3.5 3.3 - - - +
160A LEU* 2.8 45.2 + - + +
162A ASN* 3.6 23.3 - - - +
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Residues in contact with THR 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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55A TYR* 4.1 3.8 - - - -
56A TYR* 2.8 35.3 + - + +
58A PHE* 5.6 2.9 - - + -
116A VAL* 5.6 1.3 - - + -
117A TYR* 1.3 78.2 - - - +
119A ASN* 1.3 62.9 + - - +
120A ASN 3.2 15.3 + - - +
121A LEU* 3.7 29.8 - - + -
127A ARG* 3.3 17.0 + - - -
154A ILE* 4.4 5.2 - - - +
158A VAL 3.5 11.0 + - - -
159A VAL* 3.9 14.6 - - + +
205A PHE* 3.9 8.9 + - + +
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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