Contacts of the strand formed by residues 110 - 121 (chain A) in PDB entry 4HE2
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 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A TYR* 4.5 2.9 - - - +
91A THR 3.4 10.8 - - - +
92A CYS* 3.7 16.8 - - + +
104A ILE* 3.9 13.1 - - - +
105A THR* 2.9 29.7 + - - -
106A ALA* 3.2 3.0 + - - +
107A LYS* 3.2 48.3 + - + +
108A GLU 3.5 1.0 + - - -
109A LYS* 1.3 76.4 - - - +
111A GLY* 1.3 61.9 + - - +
146A GLU* 3.2 25.7 + - - -
147A PRO* 3.6 24.3 - - - +
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Residues in contact with GLY 111 (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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29A GLU* 3.1 13.5 - - - -
89A TYR 3.8 5.4 - - - -
90A SER 3.6 11.0 - - - -
91A THR 2.8 10.3 + - - +
92A CYS* 3.3 23.7 - - - +
109A LYS 3.5 2.6 + - - -
110A ARG* 1.3 76.3 - - - +
112A LYS* 1.3 61.1 + - - -
113A TYR 3.5 2.5 - - - -
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Residues in contact with LYS 112 (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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27A THR* 4.7 4.3 + - - +
29A GLU* 2.7 36.0 + - - +
92A CYS* 4.1 4.9 - - - -
111A GLY* 1.3 72.6 - - - -
113A TYR* 1.3 70.8 + - + +
140A ARG* 3.7 26.2 - - + +
141A LYS* 2.8 36.3 + - + +
401A AMP 2.8 40.1 + - - +
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Residues in contact with TYR 113 (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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29A GLU* 3.9 8.3 - - + -
30A LEU* 3.8 23.6 - - + +
33A LEU* 3.4 25.8 - - + -
90A SER 2.9 18.9 + - - +
91A THR* 3.2 8.6 - - - -
92A CYS* 2.8 29.0 + - - -
93A VAL 3.7 0.5 + - - -
111A GLY 3.5 0.6 - - - -
112A LYS* 1.3 98.1 + - + +
114A VAL* 1.3 61.8 + - - +
115A VAL* 4.9 0.2 - - - -
138A ILE* 3.8 13.0 - - + -
139A TYR 3.3 16.6 - - - +
140A ARG* 3.9 17.9 - - + -
160A VAL* 4.2 12.3 - - + -
401A AMP 2.4 59.3 + - - -
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Residues in contact with VAL 114 (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 CYS* 4.0 14.8 - - - -
93A VAL* 3.2 17.7 - - + +
113A TYR* 1.3 76.9 - - - +
115A VAL* 1.3 68.4 + - - +
116A CYS* 4.7 4.0 - - - -
137A ALA 3.8 0.3 - - - +
138A ILE* 3.3 4.0 - - - +
139A TYR* 2.8 45.8 + - + +
140A ARG 4.7 0.9 - - - -
141A LYS* 4.3 13.2 - - - +
151A ASP* 3.8 28.7 - - + +
152A ALA* 3.8 34.5 - - + -
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Residues in contact with VAL 115 (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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33A LEU* 3.8 33.7 - - + -
37A MET* 4.9 3.8 - - - -
85A LEU* 3.8 22.7 - - + -
91A THR* 4.3 4.5 - - + -
93A VAL 3.0 7.5 + - - -
94A LEU* 3.3 24.9 - - + +
95A VAL 2.9 24.1 + - - +
114A VAL* 1.3 78.3 - - - +
116A CYS* 1.3 69.1 + - - +
117A PHE* 4.1 7.8 - - + -
136A PHE* 4.5 10.5 - - + -
137A ALA 3.4 9.0 - - - +
138A ILE* 4.1 12.3 - - + -
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Residues in contact with CYS 116 (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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95A VAL* 3.3 9.4 - - + +
114A VAL* 4.7 1.6 - - - -
115A VAL* 1.3 75.0 - - - +
117A PHE* 1.3 61.1 + - - +
136A PHE* 3.3 3.6 - - - +
137A ALA* 2.8 36.3 + - + +
139A TYR* 4.2 21.5 - - - -
152A ALA* 4.2 17.7 - - - -
278A LEU* 3.5 53.6 - - + +
279A TYR* 3.8 5.4 - - + +
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Residues in contact with PHE 117 (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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37A MET* 4.8 4.0 - - + -
78A ASN* 3.3 22.2 - - - -
81A VAL* 3.6 37.2 - - + -
82A ILE* 3.8 15.3 - - + -
85A LEU* 4.2 4.9 - - + -
94A LEU* 4.2 21.1 - - + -
95A VAL 2.8 21.4 + - - -
96A SER* 3.3 25.0 - - - -
97A GLU 3.3 22.7 + - - -
115A VAL* 4.1 16.4 - - + -
116A CYS* 1.3 76.6 - - - +
118A ASP* 1.3 59.6 + - - +
119A PRO* 3.8 18.4 - - + -
135A ILE 3.1 13.0 - - - +
136A PHE* 4.0 9.9 - - + -
279A TYR* 3.4 12.6 - - - +
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Residues in contact with ASP 118 (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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97A GLU* 2.8 7.5 - - - +
117A PHE* 1.3 72.4 - - - +
119A PRO* 1.3 66.8 - - - +
120A LEU 3.1 5.4 + - - +
121A ASP* 3.5 10.4 - - - +
134A THR* 3.4 3.1 - - - +
135A ILE* 2.8 35.5 + - + -
279A TYR* 3.6 23.0 - - + +
280A GLU* 3.0 6.2 - - - +
402A PO3 3.4 0.4 - - - -
403A MG 2.3 9.2 - - - -
404A ZN 2.1 32.5 - - - -
405A MG 2.2 23.0 - - - -
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Residues in contact with PRO 119 (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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44A ILE* 3.9 1.9 - - - +
74A ASP* 4.3 3.1 - - - +
77A SER* 3.6 15.9 + - - +
78A ASN* 3.7 42.6 - - + +
81A VAL* 4.5 3.1 - - + -
96A SER* 3.8 15.0 - - - +
97A GLU* 4.5 3.6 - - + +
98A GLU* 3.8 22.2 - - + +
117A PHE* 3.8 15.9 - - + +
118A ASP* 1.3 88.0 - - - +
120A LEU* 1.3 60.2 + - + +
134A THR* 2.7 30.7 + - + +
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Residues in contact with LEU 120 (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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44A ILE* 4.2 14.1 - - + -
48A VAL* 4.3 6.3 - - + -
73A LEU* 4.6 9.0 - - + +
74A ASP* 3.5 21.2 - - - +
77A SER* 4.0 21.3 - - - +
118A ASP* 3.2 1.1 - - - -
119A PRO* 1.3 83.9 - - - +
121A ASP* 1.3 68.0 + - - +
123A SER* 3.6 7.7 + - - +
126A ILE* 3.9 28.9 - - + -
132A ILE* 4.1 24.5 - - + -
133A GLY 3.1 10.8 - - - +
167A TYR* 4.4 3.4 - - + -
402A PO3 3.1 0.7 + - - -
405A MG 2.2 27.4 - - - -
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Residues in contact with ASP 121 (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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118A ASP* 3.6 7.4 - - - +
120A LEU* 1.3 72.9 - - - +
122A GLY* 1.3 64.5 + - - +
132A ILE* 3.3 9.2 - - - +
133A GLY* 2.6 39.3 + - - +
135A ILE* 3.6 23.7 - - + +
248A MET* 3.4 17.0 + - - +
249A VAL* 2.9 35.5 + - - +
275A LEU* 5.9 0.5 - - - +
280A GLU* 3.7 1.6 - - - +
402A PO3 3.2 4.8 + - - -
403A MG 1.9 30.5 - - - -
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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