Contacts of the strand formed by residues 126 - 134 (chain A) in PDB entry 5Z8N
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 ASP 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A LYS* 3.2 30.3 + - - +
109A ILE* 3.7 16.6 - - - +
111A HIS* 3.2 27.4 + - + -
116A TYR* 4.7 6.1 - - + -
119A LEU* 4.2 15.3 - - + +
121A ASN 4.0 4.2 - - - +
122A VAL* 3.6 14.6 - - + +
123A GLY* 2.6 34.4 + - - +
125A GLU* 1.3 87.0 - - - +
127A TYR* 1.3 60.4 + - - +
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Residues in contact with TYR 127 (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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38A LEU* 4.6 12.9 - - + +
47A PRO* 5.9 1.9 - - - +
48A PRO* 4.9 9.0 + - - +
50A VAL* 3.9 21.1 - - + +
73A ARG* 6.4 1.8 - - - -
88A LYS* 3.9 35.4 - - + +
90A LEU* 3.5 36.3 - - + -
108A CYS* 4.4 9.0 - - + -
109A ILE 2.9 13.9 + - - +
110A VAL* 3.8 12.6 - - + -
111A HIS* 2.8 28.1 + - - -
116A TYR* 3.6 5.0 - - - -
124A ALA 3.4 18.3 + - - -
125A GLU 3.6 9.2 - - - -
126A ASP* 1.3 80.8 - - - +
128A TYR* 1.3 64.1 + - - +
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Residues in contact with TYR 128 (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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86A GLY* 3.6 5.9 + - - -
88A LYS* 3.1 21.6 + - - +
89A GLU* 3.0 53.6 + - + +
90A LEU* 2.9 27.0 + - - +
110A VAL* 4.1 3.1 - - - -
111A HIS 3.2 12.1 - - - +
112A THR 4.3 0.9 - - - +
113A PHE* 3.3 35.0 - + - -
116A TYR* 3.5 41.5 - + + -
127A TYR* 1.3 79.9 - - - +
129A CYS* 1.3 66.4 + - - +
130A ARG* 3.7 6.2 + - + -
157A PRO* 3.2 39.5 - - + +
158A ASP* 5.8 0.2 - - - -
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Residues in contact with CYS 129 (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 TYR* 4.6 3.8 - - + -
89A GLU* 5.5 0.2 - - - -
90A LEU* 3.2 20.4 - - + +
92A LEU* 3.6 19.1 - - - -
110A VAL* 4.1 15.7 - - + -
111A HIS 3.0 10.4 + - - +
112A THR* 4.1 4.0 - - - +
113A PHE 3.7 14.4 + - - -
114A LYS* 5.5 0.5 + - - -
128A TYR* 1.3 79.5 - - - +
130A ARG* 1.3 61.4 + - - +
131A PHE 3.1 30.3 - - - -
132A GLU* 6.0 0.4 - - - -
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Residues in contact with ARG 130 (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 PHE* 2.9 29.9 + - - -
89A GLU* 2.4 35.2 + - - +
90A LEU 4.1 2.0 + - - -
113A PHE* 3.8 39.7 - - + -
114A LYS* 5.5 4.3 - - - +
128A TYR* 3.7 19.8 + - + -
129A CYS* 1.3 75.2 - - - +
131A PHE* 1.3 93.5 + - + +
142A PRO* 3.6 13.5 - - - +
145A VAL* 4.6 14.2 - - - +
154A PRO* 5.0 0.4 - - - +
155A TYR* 2.7 35.7 + - - +
157A PRO* 4.3 0.2 - - - +
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Residues in contact with PHE 131 (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 PHE* 4.7 12.8 - + - -
85A HIS* 5.4 1.8 - - - -
89A GLU* 4.2 3.1 - - - -
90A LEU 4.5 0.6 + - - -
91A PHE* 3.3 27.9 - + + -
92A LEU 3.1 21.1 + - - -
129A CYS* 3.1 11.3 - - - -
130A ARG* 1.3 117.7 - - + +
132A GLU* 1.3 60.6 + - - +
140A PHE* 3.8 29.8 - + + -
141A THR 3.5 3.8 - - - +
142A PRO* 3.8 36.1 - - + -
143A ASP 5.9 0.2 - - - -
144A ARG 4.9 1.8 - - - -
145A VAL* 4.2 33.9 - - + -
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Residues in contact with GLU 132 (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 ARG* 4.4 10.8 + - - +
92A LEU* 3.4 33.3 - - + +
129A CYS* 6.0 0.4 - - - -
131A PHE* 1.3 73.6 - - - +
133A TYR* 1.3 60.1 + - - +
134A LYS 4.1 1.0 + - - -
139A ALA 3.9 0.3 - - - +
140A PHE* 3.6 4.5 - - - -
141A THR* 2.9 48.9 + - - +
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Residues in contact with TYR 133 (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 TYR* 3.7 36.6 - + + -
76A GLU 4.9 1.1 + - - -
77A SER* 4.0 13.9 - - - -
78A LEU* 3.2 27.4 + - + +
91A PHE* 3.5 20.2 - - + -
92A LEU 2.7 11.0 + - - +
93A SER* 3.5 20.4 - - - -
94A ASP* 3.9 2.7 + - - -
132A GLU* 1.3 74.7 - - - +
134A LYS* 1.3 74.4 + - - +
135A ALA* 3.4 20.9 + - - -
138A GLY* 3.4 23.6 - - - -
139A ALA 3.2 14.1 - - - -
140A PHE* 3.4 27.4 - + + -
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Residues in contact with LYS 134 (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 ASP* 2.5 37.2 + - + +
132A GLU 4.1 1.0 + - - -
133A TYR* 1.3 71.5 - - - +
135A ALA* 1.3 55.0 + - - +
136A ALA* 3.3 37.1 - - - +
137A THR* 3.1 33.7 - - + +
138A GLY* 2.8 30.3 + - - -
139A ALA* 2.9 23.6 + - + +
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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