Contacts of the strand formed by residues 90 - 97 (chain A) in PDB entry 1SSF
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 GLU 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ARG* 4.9 0.3 - - - -
86A LYS* 4.0 1.0 - - - +
87A GLU* 2.9 68.5 + - + +
88A SER 3.8 0.2 - - - -
89A GLY* 1.4 76.1 - - - +
91A LEU* 1.4 64.2 + - - +
92A TYR* 3.7 28.9 + - + -
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Residues in contact with LEU 91 (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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28A LYS* 5.7 1.3 - - + -
43A ASP* 3.6 32.8 - - + +
85A ARG 3.5 14.6 - - - +
86A LYS* 4.2 18.6 - - + -
90A GLU* 1.4 76.3 - - - +
92A TYR* 1.4 85.9 + - - +
93A TYR* 4.8 1.3 - - + -
105A LYS* 3.3 29.3 + - + +
106A ARG* 3.6 60.8 - - + +
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Residues in contact with TYR 92 (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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84A HIS* 3.5 3.3 - - - +
85A ARG* 3.0 80.1 + - + +
87A GLU* 4.1 6.8 + - - -
90A GLU* 3.7 34.3 + - + -
91A LEU* 1.4 79.8 - - - +
93A TYR* 1.4 60.9 + - - +
103A TRP* 3.5 52.0 - + + -
104A TYR 3.7 7.2 - - - +
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Residues in contact with TYR 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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13A ARG* 5.1 1.3 - - - -
59A ASP 4.2 2.5 - - - -
60A PRO* 3.2 46.9 - - + +
61A ILE* 3.6 7.7 + - + -
81A VAL* 3.8 15.0 - - + -
84A HIS* 2.7 59.1 + + + -
85A ARG 5.4 0.2 - - - -
91A LEU* 4.7 2.7 - - + +
92A TYR* 1.4 72.3 - - - +
94A SER* 1.4 59.4 + - - +
95A ILE* 3.5 27.5 - - + +
102A LYS 3.1 4.5 - - - +
103A TRP* 3.4 2.2 - - - -
104A TYR 2.8 34.0 + - - +
106A ARG* 3.7 28.3 - - + -
109A VAL* 3.9 14.1 - - + -
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Residues in contact with SER 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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80A VAL 3.6 1.4 - - - +
81A VAL* 3.7 3.6 - - - +
82A LYS* 3.2 27.6 + - - +
83A GLY* 2.6 41.5 + - - +
84A HIS* 4.6 0.6 - - - +
93A TYR* 1.4 68.6 - - - +
95A ILE* 1.3 61.3 + - - +
96A GLU* 3.9 0.4 + - - -
101A ARG* 4.4 17.0 - - - +
102A LYS 3.4 4.7 - - - -
103A TRP* 3.3 33.9 - - - -
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Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A VAL* 5.0 1.8 - - + +
68A THR 5.5 0.4 - - - +
69A ALA* 4.8 10.5 - - + -
79A GLY* 4.0 25.8 - - - +
80A VAL 3.5 4.7 - - - +
81A VAL* 4.5 8.7 - - + +
93A TYR* 3.5 45.1 - - + +
94A SER* 1.3 73.3 - - - +
96A GLU* 1.4 63.1 + - - +
97A LYS* 3.4 7.6 + - + +
101A ARG* 4.5 0.9 - - - -
102A LYS* 2.8 38.9 + - + +
104A TYR* 4.0 11.9 - - + -
109A VAL* 3.3 36.8 - - + -
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Residues in contact with GLU 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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79A GLY* 3.3 3.5 - - - -
80A VAL* 2.7 49.3 + - + +
82A LYS* 3.3 41.3 + - + +
94A SER 3.9 1.0 + - - -
95A ILE* 1.4 67.7 - - - +
97A LYS* 1.3 60.6 + - - +
98A GLU 4.6 0.3 + - - -
99A GLY* 3.5 27.4 + - - -
100A GLN 3.5 4.5 - - - +
101A ARG* 3.5 35.2 - - + +
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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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69A ALA* 4.4 17.2 - - + +
71A SER* 5.6 0.2 + - - -
77A SER* 3.6 28.7 - - - -
78A ALA 3.4 26.7 + - - +
79A GLY* 4.2 6.5 - - - -
95A ILE* 3.8 14.1 - - + +
96A GLU* 1.3 76.5 + - - +
98A GLU* 1.4 68.7 + - + +
99A GLY 3.1 4.7 - - - -
100A GLN* 2.6 46.5 + - - +
102A LYS* 3.7 37.5 - - + +
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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