Contacts of the strand formed by residues 93 - 99 (chain A) in PDB entry 4YIH
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 THR 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A SER* 4.0 0.2 + - - -
5A VAL* 3.4 10.5 - - + +
7A VAL* 4.6 4.7 - - + -
87A MET* 3.4 27.1 - - + +
88A ASN* 4.0 11.4 - - - +
90A LEU* 3.4 18.1 - - + +
91A PRO 2.8 15.4 + - - -
92A ASP* 1.3 76.7 + - - +
94A GLN* 1.3 80.7 + - - +
191A LEU* 3.7 27.1 - - + -
195A ARG* 3.0 18.3 + - - +
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Residues in contact with GLN 94 (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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4A SER* 4.4 12.7 + - - +
5A VAL 2.9 10.1 + - - +
6A ARG* 3.3 10.2 - - + +
7A VAL* 2.9 28.8 + - - +
88A ASN* 3.5 2.5 - - - +
93A THR* 1.3 83.8 + - - +
95A VAL* 1.3 61.1 + - - +
96A PHE* 4.7 1.3 - - + -
127A ARG* 2.6 40.5 + - - +
152B GLN* 3.4 38.5 - - - +
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Residues in contact with VAL 95 (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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7A VAL* 3.4 4.5 - - + +
9A VAL* 4.0 17.5 - - + -
84A VAL* 4.4 8.1 - - + +
87A MET* 3.6 38.6 - - + -
88A ASN* 3.2 33.3 + - + +
93A THR* 5.0 0.4 - - + -
94A GLN* 1.3 76.9 - - - +
96A PHE* 1.3 73.9 + - - +
97A ILE* 4.8 4.5 - - + +
124A PHE* 4.3 16.6 - - + -
127A ARG* 2.9 30.8 + - - +
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Residues in contact with PHE 96 (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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6A ARG* 3.8 27.1 - - + -
7A VAL 3.0 7.1 + - - +
8A LEU* 3.5 17.4 - - + -
9A VAL* 2.9 27.5 + - - +
94A GLN* 4.7 0.9 - - + -
95A VAL* 1.3 77.8 - - - +
97A ILE* 1.3 64.5 + - - +
98A CYS 5.1 0.2 - - - +
126A GLU 4.9 3.4 - - - -
127A ARG* 3.3 39.3 - - - +
129A ILE* 3.6 29.4 - - + -
131B THR* 5.0 1.6 - - - -
132B ARG 6.3 0.2 - - - -
133B ASP* 4.0 28.3 - - + -
136B VAL* 4.5 5.2 - - + -
152B GLN* 3.4 40.8 - - - -
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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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9A VAL* 3.3 11.9 - - + +
11A MET* 3.9 33.7 - - + -
15A LEU* 4.1 15.0 - - + -
84A VAL* 6.4 1.1 - - + -
95A VAL* 4.9 5.6 - - + -
96A PHE* 1.3 73.1 - - - +
98A CYS* 1.3 56.1 + - - +
99A THR* 4.0 4.2 + - + -
116A VAL* 3.9 33.4 - - + -
120A LEU* 4.0 12.8 - - + -
124A PHE* 4.0 28.9 - - + +
127A ARG 2.8 13.1 + - - +
128A ILE* 3.3 9.6 - - + +
129A ILE 2.8 33.0 + - - +
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Residues in contact with CYS 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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8A LEU* 4.0 28.9 - - + -
9A VAL 2.9 9.8 + - - +
10A ASP* 3.3 13.3 + - - -
96A PHE 3.6 1.8 + - - +
97A ILE* 1.3 71.8 - - - +
99A THR* 1.4 60.1 + - - +
129A ILE* 3.4 11.4 - - + -
131A THR* 3.9 16.6 - - - -
134A LYS* 3.1 46.3 + - - +
137A VAL* 4.1 21.5 - - - -
142A LEU* 4.9 2.6 - - + +
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Residues in contact with THR 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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10A ASP* 4.5 2.3 + - - -
11A MET* 3.6 37.6 + - - +
12A ASP* 4.5 1.4 + - - -
97A ILE* 4.7 3.8 - - + +
98A CYS* 1.4 74.9 - - - +
100A SER* 1.3 62.6 + - - +
112A LYS* 2.8 30.0 + - + -
128A ILE* 4.6 11.7 - - + -
129A ILE 3.0 10.9 + - - +
130A LEU* 3.2 26.3 - - + +
131A THR* 3.0 23.2 + - - -
134A LYS* 4.0 7.0 - - - +
203A 2O2 5.0 1.6 + - - -
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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