Contacts of the strand formed by residues 85 - 93 (chain A) in PDB entry 1CZS
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 VAL 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A THR* 5.1 0.7 + - - +
75A GLY* 5.2 0.2 - - - -
84A TYR* 1.3 73.2 - - - +
86A LYS* 1.3 59.7 + - - +
87A SER 3.2 28.7 - - - +
88A TYR* 4.0 14.1 - - + -
115A GLY* 3.8 2.1 - - - -
116A ASN* 2.9 28.7 + - - +
138A VAL* 5.7 0.4 - - + -
140A PRO* 4.1 17.3 - - + -
142A THR 3.5 8.5 - - - +
143A TRP* 4.1 2.0 - - + -
147A ILE* 4.1 16.8 - - + -
148A THR 3.6 27.9 + - - +
149A LEU* 3.8 25.1 - - + +
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Residues in contact with LYS 86 (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 TYR* 3.6 25.3 + - + +
85A VAL* 1.3 74.1 - - - +
87A SER* 1.3 53.7 + - - -
114A GLU* 4.0 7.4 - - - +
115A GLY* 2.7 26.9 + - - +
116A ASN 3.6 9.4 - - - +
142A THR* 2.8 28.0 + - - +
143A TRP* 3.5 28.7 + - - +
144A ASN* 3.8 9.4 - - + +
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Residues in contact with SER 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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85A VAL* 3.2 5.8 - - - +
86A LYS* 1.3 78.9 - - - +
88A TYR* 1.3 65.5 + - - +
112A ILE* 3.9 16.5 - - - +
113A PHE 3.1 14.4 - - - -
114A GLU* 4.7 8.5 - - - -
115A GLY 3.9 1.6 - - - +
141A LYS* 2.9 26.4 + - - +
142A THR* 2.8 34.8 + - - +
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Residues in contact with TYR 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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71A ILE* 3.7 23.6 + - + +
73A THR* 3.9 27.4 + - + +
85A VAL* 4.0 13.5 - - + -
87A SER* 1.3 82.4 + - - +
89A THR* 1.3 73.1 + - - +
90A ILE* 3.8 19.7 - - + -
112A ILE* 3.7 1.3 - - - +
113A PHE* 2.7 52.4 + + + +
114A GLU 4.7 0.2 + - - -
115A GLY* 3.9 22.7 - - - -
123A VAL* 5.0 2.4 + - - +
125A ASN* 3.2 16.3 + - - -
138A VAL* 3.9 15.9 - - + -
139A ILE 3.2 21.1 - - - +
140A PRO* 3.9 4.7 - - + -
141A LYS* 3.9 5.1 - - - +
149A LEU* 5.7 0.4 - - + -
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Residues in contact with THR 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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88A TYR* 1.3 76.0 - - - +
90A ILE* 1.3 69.6 + - - +
91A HIS* 3.9 9.9 + - - -
101A PRO* 6.1 0.2 - - - -
102A TYR 6.0 0.4 - - - -
110A ASP* 4.0 22.5 + - + +
111A LYS 3.5 14.8 - - - +
112A ILE* 3.4 32.3 - - + -
113A PHE* 4.3 0.2 - - - -
139A ILE* 2.9 51.7 + - - +
141A LYS* 3.5 19.5 - - - +
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Residues in contact with ILE 90 (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* 4.1 9.6 - - + -
88A TYR* 3.8 19.1 - - + -
89A THR* 1.3 83.6 - - - +
91A HIS* 1.3 74.6 + - - +
92A TYR* 4.9 0.2 - - + -
101A PRO* 4.3 0.2 - - - +
102A TYR* 2.7 36.4 + - + +
111A LYS 4.5 0.6 + - - -
113A PHE* 3.6 30.3 - - + -
127A PHE* 3.9 13.2 - - + -
131A ILE* 3.8 28.3 - - + -
136A ILE* 4.1 12.1 - - + -
137A ARG 3.4 11.2 - - - +
138A VAL* 4.1 15.7 - - + -
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Residues in contact with HIS 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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89A THR* 3.9 10.9 + - - -
90A ILE* 1.3 87.1 - - - +
92A TYR* 1.3 65.0 + - - +
99A TRP* 4.1 22.8 - - + +
100A LYS 3.2 9.4 - - - +
101A PRO* 3.7 22.1 - - + +
110A ASP* 4.2 7.1 + - - -
136A ILE* 3.6 1.7 - - - -
137A ARG* 2.8 45.0 + - + +
139A ILE* 3.7 33.9 - - + +
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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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91A HIS* 1.3 77.2 - - - +
93A SER* 1.3 66.1 + - - +
98A GLU 4.1 0.3 - - - +
99A TRP* 3.5 4.4 - - - -
100A LYS* 2.8 86.2 + - + +
101A PRO 3.9 1.3 + - - -
102A TYR* 3.8 33.7 - + + -
103A ARG 5.4 0.2 + - - -
131A ILE* 3.8 29.6 - - + -
132A ILE 4.5 7.2 - - - -
133A SER* 3.7 23.3 - - - +
135A PHE 3.2 13.9 - - - +
136A ILE* 4.1 4.5 - - + -
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Residues in contact with SER 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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92A TYR* 1.3 75.5 - - - +
94A GLU* 1.3 58.5 + - - +
95A GLN 3.4 0.9 + - - -
96A GLY* 2.9 24.6 + - - -
97A VAL 3.1 6.8 + - - -
98A GLU 2.8 25.7 + - - -
99A TRP* 3.7 19.5 - - - -
133A SER* 2.7 21.3 + - - -
134A ARG 3.2 0.2 + - - -
135A PHE* 2.9 29.0 + - - -
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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