Contacts of the strand formed by residues 92 - 100 (chain A) in PDB entry 1S9J
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 LEU 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A SER* 3.8 1.9 - - - -
87A HIS* 3.1 27.9 + - + +
90A SER* 3.1 25.4 + - - +
91A GLY* 1.3 77.8 - - - +
93A VAL* 1.3 77.0 + - - +
94A MET* 3.7 10.5 + - + +
130A TYR* 4.3 34.5 - - + +
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Residues in contact with VAL 93 (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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71A ILE* 4.5 10.8 - - + -
84A LYS* 4.0 26.7 - - + +
85A VAL 3.5 13.7 - - - +
86A SER* 5.3 3.6 - - - +
91A GLY 3.7 5.1 + - - +
92A LEU* 1.3 84.7 - - - +
94A MET* 1.3 66.0 + - - +
130A TYR* 5.0 2.8 + - - -
145A HIS* 3.8 33.8 + - + +
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Residues in contact with MET 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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63A LEU* 4.1 4.9 - - + -
68A PHE* 3.3 35.2 - - + -
84A LYS* 3.6 5.2 - - - -
85A VAL* 3.0 37.3 + - + +
87A HIS* 4.3 12.1 - - + -
92A LEU* 3.9 16.8 - - + +
93A VAL* 1.3 81.7 - - - +
95A ALA* 1.3 62.2 + - - +
130A TYR* 3.3 38.4 - - + -
142A CYS* 3.5 26.9 - - + -
143A MET 3.6 9.4 - - - +
145A HIS* 3.9 10.5 - - - +
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Residues in contact with ALA 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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74A LEU* 3.7 15.9 - - + -
82A VAL* 4.7 1.6 - - + -
83A PHE 3.4 4.7 - - - -
94A MET* 1.3 75.5 - - - +
96A ARG* 1.3 60.2 + - - +
97A LYS 4.0 0.7 - - - -
141A ILE 3.6 0.7 - - - +
142A CYS* 3.5 4.3 - - - -
143A MET* 3.0 40.1 + - + +
144A GLU 4.2 1.3 - - - +
145A HIS* 4.2 2.2 - - - +
535A ATP 3.4 39.9 - - + +
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Residues in contact with ARG 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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65A ASP* 3.2 28.1 + - - -
68A PHE* 4.1 26.9 - - - +
70A LYS* 6.2 4.0 - - - +
81A VAL 4.1 0.7 - - - +
82A VAL* 3.4 5.0 - - - +
83A PHE* 3.0 35.1 + - + +
85A VAL* 3.9 29.5 - - + +
95A ALA* 1.3 74.0 - - - +
97A LYS* 1.3 60.7 + - - +
98A LEU* 3.7 20.9 + - + +
133A PHE* 3.3 26.2 - - - -
135A SER* 4.3 5.1 - - - -
140A SER* 3.1 29.5 + - - +
141A ILE 3.7 2.5 - - - +
142A CYS* 4.1 17.3 - - - +
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Residues in contact with LYS 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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80A GLY 5.3 1.8 - - - +
81A VAL 5.0 0.4 - - - +
82A VAL* 4.0 18.9 - - + +
95A ALA 4.0 1.4 - - - -
96A ARG* 1.3 72.1 - - - +
98A LEU* 1.3 65.8 + - - +
99A ILE* 3.9 21.1 + - + +
139A ILE 3.8 0.2 - - - +
140A SER* 3.5 6.2 + - - -
141A ILE* 3.1 32.9 + - + +
143A MET* 3.8 18.3 - - + +
208A ASP* 2.9 17.6 + - - -
535A ATP 2.6 40.0 + - - -
1001A BBM 2.6 57.7 + - - +
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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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70A LYS* 5.7 2.2 - - - +
80A GLY* 3.5 28.5 + - - +
81A VAL* 3.5 11.0 + - + +
83A PHE* 3.7 30.1 - - + -
96A ARG* 3.7 27.8 - - - +
97A LYS* 1.3 75.0 - - - +
99A ILE* 1.3 63.7 + - - +
100A HIS 3.9 1.0 + - - -
135A SER* 6.2 1.1 - - - -
138A GLU* 3.6 36.2 - - + +
139A ILE 3.6 4.3 - - - +
140A SER* 3.1 28.5 - - - +
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Residues in contact with ILE 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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80A GLY* 5.5 2.0 - - - +
97A LYS* 3.9 13.7 - - + -
98A LEU* 1.3 75.5 - - - +
100A HIS* 1.3 65.7 + - - +
101A LEU* 3.5 22.7 + - + +
138A GLU* 3.9 2.0 - - - -
139A ILE* 3.2 45.4 + - + +
141A ILE* 4.0 22.0 - - + -
215A LEU* 4.6 6.7 - - + -
219A MET* 3.8 32.3 - - - -
1001A BBM 3.9 30.5 - - - +
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Residues in contact with HIS 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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80A GLY* 5.7 3.9 - - - +
98A LEU 3.9 2.6 + - - -
99A ILE* 1.3 73.9 - - - +
101A LEU* 1.3 76.6 + - - +
102A GLU* 4.6 18.1 + - + +
137A GLY* 3.0 33.9 + - - -
138A GLU* 3.5 26.3 + - - +
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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