Contacts of the strand formed by residues 96 - 101 (chain A) in PDB entry 5H5Q
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 ARG 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A TYR* 3.8 23.8 - - + -
62A PHE* 3.3 35.7 - - + -
63A VAL 2.9 5.9 + - - -
64A SER* 3.2 10.8 - - - +
65A ILE 2.9 23.6 + - - -
87A HIS* 4.9 8.7 + - - -
91A ALA* 2.9 31.1 + - - +
94A GLY* 3.5 6.7 - - - -
95A LEU* 1.3 99.3 + - - +
97A ILE* 1.3 66.5 + - - +
98A LEU* 4.3 0.4 - - - -
128A ASP* 5.0 4.9 - - - +
201A GOL 2.7 48.0 + - - +
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Residues in contact with ILE 97 (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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65A ILE* 3.3 20.2 - - + +
67A THR* 4.5 7.6 - - + -
83A LEU* 3.4 50.9 - - + +
86A LEU* 4.5 2.9 - - + -
87A HIS* 4.0 18.6 - - + +
95A LEU* 4.3 14.6 - - + -
96A ARG* 1.3 81.1 - - - +
98A LEU* 1.3 68.8 + - - +
99A ALA 4.0 0.2 - - - -
127A PHE* 3.5 35.6 - - + +
128A ASP* 3.0 33.2 + - - +
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Residues in contact with LEU 98 (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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41A MET* 4.4 4.5 - - + -
56A LEU* 4.1 16.6 - - + -
59A TYR* 3.6 48.7 - - + -
64A SER* 3.9 25.6 - - - -
65A ILE 2.8 12.8 + - - +
66A VAL* 3.4 15.3 - - + -
67A THR* 3.0 26.7 + - - +
97A ILE* 1.3 78.3 - - - +
99A ALA* 1.3 59.6 + - - +
100A PHE* 4.0 19.2 + - + -
128A ASP 3.6 3.8 - - - -
130A PHE* 3.7 20.6 - - + -
143A LEU* 5.1 0.4 - - + -
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Residues in contact with ALA 99 (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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67A THR* 3.5 9.0 - - + -
69A VAL* 3.9 19.3 - - + -
80A TYR* 5.7 0.2 - - + -
98A LEU* 1.3 71.9 - - - +
100A PHE* 1.3 60.6 + - - +
101A PRO* 3.5 4.4 - - - +
127A PHE* 3.9 16.2 - - + -
128A ASP 2.9 10.5 + - - +
129A MET* 3.7 27.6 - - + +
130A PHE* 2.9 30.6 + - - +
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Residues in contact with PHE 100 (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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46A ALA* 3.8 21.8 - - + -
56A LEU* 4.9 1.3 - - + -
66A VAL* 3.9 25.6 - - + -
67A THR 2.8 12.2 + - - +
68A ASN* 3.1 7.5 - - + +
69A VAL* 2.9 21.2 + - - +
98A LEU* 4.0 20.0 - - + -
99A ALA* 1.3 74.3 - - - +
101A PRO* 1.3 69.5 - - - +
102A SER* 4.5 0.2 - - - -
130A PHE* 3.6 35.9 - + + -
131A SER 4.4 3.6 - - - -
133A ILE* 3.5 36.1 - - + -
141A HIS* 4.9 6.7 - + - -
143A LEU* 4.2 16.8 - - + -
144A TRP* 3.5 20.4 - + + +
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Residues in contact with PRO 101 (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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49A ILE* 4.4 2.7 - - + -
69A VAL* 3.4 15.7 - - + +
99A ALA 3.5 6.1 - - - +
100A PHE* 1.3 85.4 - - - +
102A SER* 1.3 59.5 - - - +
109A GLU* 3.4 23.6 - - + +
116A ILE* 3.8 26.2 - - + -
129A MET* 4.5 2.2 - - + -
130A PHE 2.9 31.6 - - - +
131A SER 3.9 4.3 - - - +
132A LYS* 3.9 12.1 - - - +
133A ILE* 2.9 26.5 + - - +
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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