Contacts of the strand formed by residues 152 - 162 (chain A) in PDB entry 3ZUD
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 GLY 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ALA 3.9 0.6 + - - -
151A PRO* 1.3 74.3 - - - +
153A ASN* 1.3 66.7 + - - -
154A TYR* 3.3 12.3 - - - -
182A GLN* 4.5 2.7 - - - -
183A VAL 2.8 33.7 + - - -
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Residues in contact with ASN 153 (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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66A THR* 4.2 9.0 - - + +
96A PRO* 3.6 2.1 - - - +
97A CYS* 2.8 22.9 + - - +
98A ASN 4.2 1.8 + - - +
99A GLY* 3.0 34.4 + - - +
100A ASP* 4.2 5.3 - - - +
101A CYS* 3.6 16.2 - - - +
152A GLY* 1.3 73.8 - - - -
154A TYR* 1.3 65.0 + - - +
181A LEU 3.3 5.3 - - - +
182A GLN* 3.7 29.1 + - - +
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Residues in contact with TYR 154 (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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94A LEU* 3.8 27.4 - - + -
95A ALA 3.2 8.1 - - - +
96A PRO* 3.5 38.2 - - + +
97A CYS* 3.9 0.7 - - - -
101A CYS* 3.6 6.8 - - - -
112A PHE* 3.9 22.6 - + - -
149A ILE* 4.2 11.4 - - + +
150A ALA* 2.6 41.8 + - - +
151A PRO 4.2 0.8 + - - -
152A GLY* 3.3 30.7 - - - -
153A ASN* 1.3 75.4 - - - +
155A VAL* 1.3 59.7 + - - +
156A LEU 3.8 0.3 + - - -
180A ASN* 3.7 1.7 - - - -
181A LEU* 2.8 36.9 + - + +
183A VAL* 3.5 22.2 - - + -
189A ASP 4.6 1.9 + - - -
190A ASN* 4.6 4.2 + - - -
191A PRO* 5.6 0.9 - - - +
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Residues in contact with VAL 155 (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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34A TRP* 3.7 25.4 - - + +
56A CYS* 4.2 5.4 - - - -
93A TYR 3.7 0.5 - - - +
94A LEU* 3.2 7.8 - - - -
95A ALA* 2.9 32.4 + - - +
97A CYS* 3.6 20.6 - - - -
101A CYS* 4.6 0.4 - - + -
104A VAL* 4.7 0.7 - - + -
109A LEU* 4.0 18.8 - - + -
111A PHE* 4.5 9.8 - - + -
154A TYR* 1.3 72.5 - - - +
156A LEU* 1.3 61.7 + - - +
157A ARG 3.8 1.0 + - - +
178A CYS* 3.8 36.6 - - + -
179A ILE 3.4 7.2 - - - +
180A ASN* 4.0 6.5 - - - +
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Residues in contact with LEU 156 (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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75A VAL* 4.2 10.5 - - + -
77A LEU* 4.2 25.6 - - + -
92A ASN* 4.1 16.6 - - + +
93A TYR 3.4 17.0 - - - +
94A LEU* 3.9 13.2 - - + +
114A ILE* 4.3 14.1 - - + -
143A VAL* 4.5 8.7 - - + -
145A ILE* 5.1 0.4 - - + -
154A TYR 3.8 2.2 + - - -
155A VAL* 1.3 71.0 - - - +
157A ARG* 1.3 62.2 + - - +
158A HIS* 4.5 2.9 - - + +
177A GLN 3.6 1.6 - - - +
178A CYS* 3.1 5.5 - - - +
179A ILE* 2.9 60.3 + - + +
181A LEU* 3.8 22.0 - - + -
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Residues in contact with ARG 157 (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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54A ILE* 2.8 33.5 + - - +
55A ILE* 2.8 28.1 + - - +
92A ASN* 3.5 2.9 - - - -
93A TYR* 2.9 60.7 + - + +
111A PHE* 3.7 34.8 - - + -
155A VAL 3.8 1.2 + - - -
156A LEU* 1.3 72.2 - - - +
158A HIS* 1.3 59.2 + - - +
159A GLU* 2.8 46.3 + - - +
176A PRO* 3.6 14.1 - - + +
177A GLN 3.7 3.1 - - - -
178A CYS* 3.9 9.4 - - - -
199A LEU* 3.7 20.6 - - - +
200A TYR* 3.9 3.0 - - - -
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Residues in contact with HIS 158 (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 VAL* 4.1 4.0 - - + -
77A LEU* 3.9 35.6 - - + +
79A TRP* 2.8 47.6 + + - -
90A VAL* 3.7 14.9 - - + +
91A ILE 3.7 0.2 - - - -
92A ASN* 2.8 27.5 + - - +
134A LEU* 4.7 0.4 - - + +
141A TRP* 3.5 37.9 - + + +
156A LEU* 4.6 5.6 - - + -
157A ARG* 1.3 71.8 - - - +
159A GLU* 1.3 62.3 + - - +
160A ILE* 5.2 0.2 - - - +
175A TYR 3.7 1.6 - - - +
176A PRO* 3.5 0.7 - - - +
177A GLN* 2.8 40.2 + - + +
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Residues in contact with GLU 159 (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 TRP* 5.0 0.9 - - - -
89A PRO 3.9 0.3 - - - +
90A VAL* 3.3 7.5 - - - +
91A ILE* 2.9 41.1 + - + +
93A TYR* 4.0 1.7 - - - -
157A ARG* 2.8 38.4 + - - +
158A HIS* 1.3 79.1 - - - +
160A ILE* 1.3 77.6 + - - +
161A ILE* 3.9 6.7 + - + +
174A ASN* 2.9 31.3 - - - +
175A TYR 3.4 13.9 - - - +
176A PRO* 4.0 3.1 - - + +
200A TYR* 2.5 29.1 + - - -
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Residues in contact with ILE 160 (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 TRP* 3.6 37.0 - - + +
82A TRP* 3.6 56.1 - - + +
86A HIS 4.7 0.9 - - - +
89A PRO 3.4 10.3 - - - +
90A VAL* 4.2 7.6 - - + -
131A SER* 4.4 12.8 - - - -
134A LEU* 3.8 23.1 - - + -
159A GLU* 1.3 76.5 - - - +
161A ILE* 1.3 70.7 + - - +
162A ALA 4.0 0.4 - - - +
175A TYR* 2.8 36.6 + - + +
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Residues in contact with ILE 161 (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 GLY* 3.1 26.0 - - - -
89A PRO* 3.0 20.8 + - + +
91A ILE* 3.9 25.4 - - + -
159A GLU* 3.9 8.3 - - + -
160A ILE* 1.3 80.1 - - - +
162A ALA* 1.3 60.8 + - - +
163A LEU* 3.9 20.1 - - + +
172A ALA* 4.2 9.0 - - + -
173A GLN 3.3 3.8 - - - +
174A ASN* 3.6 39.5 - - - +
200A TYR* 4.0 14.6 - - + +
207A ILE* 4.1 16.4 - - + -
221A PRO* 4.3 6.3 - - + -
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Residues in contact with ALA 162 (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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82A TRP* 4.4 2.0 - - + -
86A HIS* 3.7 22.2 - - + +
87A HIS 3.7 4.0 - - - -
160A ILE* 4.0 2.0 - - - +
161A ILE* 1.3 72.4 - - - +
163A LEU* 1.3 60.4 + - - +
164A HIS* 3.5 28.0 + - + +
171A GLY 4.6 0.7 - - - +
172A ALA* 3.6 5.0 - - - -
173A GLN* 2.8 35.7 + - + +
175A TYR* 3.9 20.6 - - + -
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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