Contacts of the strand formed by residues 82 - 89 (chain A) in PDB entry 1S5E
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 82 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A SER* 4.8 6.1 - - - +
80A HIS* 3.7 12.1 + - - +
81A SER* 1.3 81.2 + - - +
83A TYR* 1.3 67.6 + - - +
84A TYR* 3.9 28.1 - - + +
129A ARG* 4.0 22.7 + - + +
130A VAL 3.2 4.0 - - - +
131A HIS* 2.9 28.6 + - - -
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Residues in contact with TYR 83 (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 ALA* 3.8 18.4 - - + -
9A ASP 3.8 8.3 - - - +
10A SER* 4.1 9.6 - - - +
70A HIS* 3.4 16.5 - - - -
73A GLY* 3.4 22.8 - - - -
74A GLN* 2.7 28.5 + - - -
77A LEU* 3.7 30.1 - - + -
78A SER* 5.9 0.4 - - - -
80A HIS* 4.2 18.8 - - + -
82A THR* 1.3 74.0 - - - +
84A TYR* 1.3 80.4 + - - +
85A ILE* 4.0 5.6 - - + -
129A ARG* 3.6 2.9 - - - +
130A VAL* 2.7 63.4 + - + -
133A GLY* 4.9 3.1 - - - -
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG 3.6 0.7 - - - +
8A ALA* 3.3 3.3 - - - -
9A ASP 2.9 32.0 + - - +
10A SER 4.4 5.6 - - - -
11A ARG 3.9 3.8 - - - -
12A PRO* 3.7 32.7 - - + +
13A PRO* 3.7 25.6 - - + +
82A THR* 3.9 20.6 - - + +
83A TYR* 1.3 83.0 - - - +
85A ILE* 1.3 64.5 + - - +
86A TYR* 3.5 27.0 - - + -
127A TRP* 4.4 9.2 - + + -
128A TYR 3.2 15.7 - - - +
129A ARG* 3.6 29.7 - - + +
140A HIS* 6.1 0.9 - + - -
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Residues in contact with ILE 85 (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 TYR* 4.3 4.3 - - + -
7A ARG 3.4 12.8 - - - +
8A ALA* 4.2 6.7 - - + -
66A LEU* 3.7 29.2 - - + -
69A ALA* 4.3 11.0 - - + -
70A HIS* 3.8 39.9 - - + +
83A TYR* 4.0 9.4 - - + -
84A TYR* 1.3 77.5 - - - +
86A TYR* 1.3 69.1 - - - +
87A VAL 3.8 0.3 + - - -
127A TRP* 3.3 2.8 - - - -
128A TYR* 2.8 42.4 + - + +
130A VAL* 3.8 23.1 - - + +
135A LEU* 4.2 4.3 - - + -
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Residues in contact with TYR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TYR* 3.2 7.3 - - - +
7A ARG 2.8 42.5 + - - +
9A ASP* 3.9 13.5 - - + -
11A ARG 2.7 29.0 + - - -
12A PRO 3.1 1.7 - - - -
13A PRO* 3.0 26.4 - - + +
16A ILE* 3.4 18.8 - - + +
22A LEU* 3.9 35.4 - - + -
84A TYR* 3.5 20.3 - + + +
85A ILE* 1.3 72.2 - - - +
87A VAL* 1.3 59.3 + - - +
88A ILE* 3.6 8.0 - - + +
124A ILE* 3.9 11.9 - - + -
126A GLY 3.6 2.0 - - - -
127A TRP* 3.8 37.7 - + + -
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Residues in contact with VAL 87 (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 LYS* 3.8 29.6 - - + -
5A LEU 3.5 3.4 - - - -
6A TYR* 4.0 18.2 - - + +
85A ILE 4.3 0.4 - - - +
86A TYR* 1.3 72.7 - - - +
88A ILE* 1.3 58.1 - - - +
124A ILE* 3.7 3.5 - - - +
125A TYR* 2.8 53.2 + - + -
126A GLY 2.9 12.1 + - - +
128A TYR* 3.8 33.7 - - + -
139A LEU* 4.0 15.9 - - + -
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Residues in contact with ILE 88 (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 LYS* 3.3 8.0 - - - -
5A LEU* 2.7 46.6 + - + +
6A TYR 4.4 0.2 - - - -
7A ARG* 3.9 22.4 - - + +
22A LEU* 4.0 9.9 - - + -
62A THR* 4.0 6.1 - - + -
86A TYR* 3.6 23.1 - - + +
87A VAL* 1.3 78.6 - - - +
89A ALA* 1.3 75.4 + - - +
94A MET* 3.6 24.5 - - + -
119A ILE* 3.8 39.0 - - + -
123A GLN* 3.6 6.1 - - + +
124A ILE* 4.5 4.7 - - + -
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Residues in contact with ALA 89 (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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3A ASP 4.0 6.7 - - - +
4A LYS* 4.1 7.1 - - + +
5A LEU* 4.6 0.6 - - - +
87A VAL 4.4 0.2 - - - -
88A ILE* 1.3 80.1 - - - +
90A THR* 1.3 61.2 + - - +
94A MET* 4.2 1.9 - - - +
123A GLN* 2.8 41.6 + - + +
125A TYR 4.9 1.4 - - - +
145A TYR* 3.9 16.2 - - + +
150A TYR* 3.6 35.7 - - + +
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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