Contacts of the strand formed by residues 83 - 91 (chain A) in PDB entry 1Z78
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 ARG 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A GLN* 4.0 0.2 - - - -
82A THR* 1.3 76.3 - - - +
84A GLY* 1.3 59.9 + - - +
85A THR 4.2 0.2 - - - -
102A VAL* 4.4 7.9 - - + -
103A SER 3.6 4.9 - - - -
104A ASN* 3.2 37.9 - - - +
105A GLY 4.3 0.2 - - - +
106A LYS* 3.4 39.4 - - + +
187A ASN 4.7 1.4 - - - +
188A ASP* 3.5 47.1 - - - +
189A ASN 3.8 4.0 - - - +
191A GLN* 5.2 2.1 - - - +
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Residues in contact with GLY 84 (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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78A GLN* 3.3 11.1 + - - -
82A THR* 5.4 0.2 - - - -
83A ARG* 1.3 74.7 - - - +
85A THR* 1.3 65.2 - - - -
86A LEU* 3.4 3.6 + - - +
102A VAL* 4.0 3.2 - - - +
103A SER* 2.8 42.2 + - - -
188A ASP 3.6 2.9 - - - -
189A ASN 4.1 0.2 - - - -
190A PHE* 3.9 20.0 - - - -
191A GLN 5.0 1.1 - - - -
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Residues in contact with THR 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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84A GLY* 1.3 70.3 - - - -
86A LEU* 1.3 60.1 + - - +
87A LEU* 3.5 26.9 - - - +
88A ALA* 4.0 4.5 - - + -
97A GLN* 5.2 0.5 + - - -
100A SER* 4.8 2.5 - - - -
101A VAL 3.6 7.6 - - - +
102A VAL* 3.6 15.6 - - + +
182A ALA* 3.1 20.8 - - - -
183A LYS 3.2 29.4 - - - +
184A GLY* 3.3 13.1 - - - -
188A ASP* 2.8 29.6 + - - +
190A PHE* 3.4 9.9 - - - +
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Residues in contact with LEU 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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72A LEU* 5.8 2.5 - - + -
74A ALA* 5.1 10.8 - - + -
76A LEU* 3.8 18.6 - - + -
84A GLY 3.7 8.5 - - - +
85A THR* 1.3 73.0 - - - +
87A LEU* 1.3 74.6 + - + +
101A VAL* 2.8 31.1 + - + +
103A SER* 4.1 5.2 - - - +
110A LEU* 4.1 15.5 - - + -
130A LEU* 5.3 0.2 - - + -
138A ILE* 4.3 16.6 - - + -
181A ILE* 3.6 10.4 - - - +
182A ALA* 2.9 20.3 + - - +
190A PHE* 3.7 31.2 - - + -
194A LEU* 4.4 14.7 - - + +
197A VAL* 5.1 8.3 - - + +
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Residues in contact with LEU 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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15A ILE* 4.5 11.9 - - + -
72A LEU* 3.8 22.2 - - + -
85A THR* 3.5 7.7 - - - +
86A LEU* 1.3 89.0 - - + +
88A ALA* 1.3 63.6 + - - +
89A LEU* 6.0 0.9 - - + -
99A PHE* 5.5 4.7 - - + -
100A SER* 3.5 0.7 - - - -
101A VAL* 3.1 60.1 + - + -
179A LEU* 4.1 13.5 - - + -
180A ARG 3.3 13.9 - - - +
181A ILE* 4.6 4.7 - - + -
182A ALA 4.3 1.1 - - - +
197A VAL* 4.5 5.8 - - + -
199A PHE* 3.6 36.3 - - + -
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Residues in contact with ALA 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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85A THR* 4.0 1.3 - - + -
87A LEU* 1.3 78.1 - - - +
89A LEU* 1.3 66.6 + - - +
90A GLU* 3.7 2.9 + - + +
97A GLN* 3.2 31.4 - - + +
99A PHE* 3.3 12.3 - - - +
100A SER* 3.9 4.5 - - - +
178A ARG 3.6 1.2 - - - +
179A LEU* 3.4 2.4 - - - +
180A ARG* 2.8 37.4 + - + +
183A LYS 3.7 13.4 + - - +
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Residues in contact with LEU 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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57A PHE* 3.8 24.7 - - + -
87A LEU* 6.0 0.7 - - + -
88A ALA* 1.3 70.4 - - - +
90A GLU* 1.3 61.2 + - - +
97A GLN* 3.3 4.8 - - - +
98A VAL* 2.8 52.6 + - + +
99A PHE* 2.8 37.6 + - + +
168A VAL* 4.3 2.2 - - + -
169A PHE* 3.9 26.0 - - + -
173A LEU* 3.9 15.0 - - + -
177A ALA* 4.6 3.6 - - + -
178A ARG 3.5 4.9 - - - +
179A LEU* 3.4 30.1 - - + -
199A PHE* 6.2 1.8 - - + -
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Residues in contact with GLU 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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88A ALA* 3.7 3.6 - - + +
89A LEU* 1.3 74.1 - - - +
91A ARG* 1.3 70.6 + - - +
92A LYS 3.4 0.2 + - - -
94A HIS* 5.2 6.8 + - - -
96A GLY 3.8 7.9 - - - +
97A GLN* 4.2 11.9 - - + +
177A ALA* 3.2 2.8 - - - -
178A ARG* 2.7 80.1 + - + +
180A ARG* 3.0 28.9 + - + +
183A LYS* 3.5 26.2 + - - +
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Residues in contact with ARG 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 LEU 3.9 0.4 + - - -
90A GLU* 1.3 79.3 - - - +
92A LYS* 1.3 63.8 + - - +
93A ASP* 2.9 36.3 + - - +
94A HIS* 3.0 19.1 + - - -
95A SER* 2.8 30.6 + - - +
96A GLY* 2.8 29.7 + - - +
97A GLN 5.4 0.9 - - - -
98A VAL* 3.7 25.8 - - + -
115A THR* 6.5 0.9 - - - -
117A GLN* 6.0 5.4 - - - +
176A ILE* 3.4 34.2 + - - +
177A ALA* 4.2 1.1 - - - +
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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