Contacts of the strand formed by residues 119 - 128 (chain A) in PDB entry 5HAN
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 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A MET* 4.1 8.1 - - + -
31A LYS 3.7 5.8 - - - +
32A PRO* 4.4 0.7 - - - -
33A LYS* 3.5 13.5 - - - -
42A THR* 3.7 24.2 - - + -
46A PHE* 4.4 9.6 - - + -
113A ASN 5.1 4.7 - - - +
116A MET* 3.3 47.9 + - + +
117A GLY 3.4 0.6 - - - -
118A ASP* 1.4 78.6 - - - +
120A GLU* 1.3 66.7 + - - +
121A TYR* 3.2 34.5 - - - +
122A ALA* 4.2 5.2 - - + +
302A ARG* 5.3 4.1 + - - +
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Residues in contact with GLU 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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31A LYS* 2.7 52.2 + - + +
32A PRO 4.0 9.1 - - - +
33A LYS* 3.6 24.7 - - + +
34A ALA* 4.9 2.8 + - - +
119A VAL* 1.3 73.9 - - - +
121A TYR* 1.3 74.2 + - + +
302A ARG* 2.8 27.3 + - - -
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Residues in contact with TYR 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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29A ILE* 4.1 19.3 - - + -
30A MET* 3.2 5.5 - - - -
31A LYS* 2.9 61.8 + - + +
80A SER* 4.8 5.7 + - - -
119A VAL* 3.2 12.6 - - - +
120A GLU* 1.3 106.3 - - + +
122A ALA* 1.3 60.5 + - - +
301A LYS* 3.4 58.0 - - + +
302A ARG* 3.9 16.6 - - + +
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Residues in contact with ALA 122 (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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28A TYR* 5.0 2.0 - - + -
29A ILE 3.2 9.0 - - - -
30A MET* 3.9 13.0 - - + -
46A PHE* 3.5 35.7 - - + -
82A MET* 4.9 0.9 - - + -
110A ILE* 5.1 0.7 - - - -
113A ASN 5.3 0.4 - - - +
114A GLN* 3.1 31.4 + - - +
119A VAL* 4.2 3.6 - - + +
121A TYR* 1.3 80.1 - - - +
123A LYS* 1.3 59.6 + - - +
301A LYS 3.4 1.5 + - - -
302A ARG* 3.5 2.9 - - - +
303A GLY 3.4 4.0 + - - -
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Residues in contact with LYS 123 (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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28A TYR* 3.2 6.8 - - - +
29A ILE* 2.9 32.5 + - + +
122A ALA* 1.3 75.0 - - - +
124A MET* 1.3 65.9 + - - +
125A TYR* 3.5 29.9 + - + +
295A VAL 3.1 20.3 + - - -
296A THR 3.4 8.3 + - - -
297A SER 2.9 19.6 + - - -
298A PRO* 4.3 3.6 - - - +
300A SER 2.9 27.2 + - - +
301A LYS* 3.5 14.1 - - - +
302A ARG 3.4 14.6 - - - +
303A GLY 3.3 8.7 - - - +
304A TYR* 3.5 18.2 - - - +
305A THR* 3.9 9.3 - - - +
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Residues in contact with MET 124 (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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26A CYS* 3.8 11.2 - - + -
27A ALA 3.5 8.3 - - - +
28A TYR* 3.8 16.2 - - + +
105A PHE* 4.1 7.2 - - + -
109A THR* 3.3 45.5 - - - +
110A ILE* 4.3 9.9 - - + -
123A LYS* 1.3 72.4 - - - +
125A TYR* 1.3 59.0 + - - +
126A ASP 3.5 24.7 - - - +
127A PHE* 4.1 15.0 - - - -
303A GLY 2.9 14.6 + - - +
304A TYR* 3.4 6.8 - - + -
305A THR* 3.3 26.7 + - - +
308A VAL* 3.6 23.3 - - + +
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Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ALA 2.9 8.3 + - - +
29A ILE* 3.5 40.7 - - + +
123A LYS* 3.5 38.2 + - + +
124A MET* 1.3 75.4 - - - +
126A ASP* 1.3 62.8 + - - +
298A PRO* 5.8 2.4 + - - +
300A SER 5.3 1.4 + - - -
301A LYS* 5.8 2.1 + - - -
305A THR* 3.8 25.6 + - + -
307A PHE* 3.8 6.9 - - - +
308A VAL* 3.5 12.2 - - - +
352A PRO* 3.5 20.6 - - + +
353A TYR* 3.8 25.6 - + + -
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Residues in contact with ASP 126 (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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26A CYS* 3.5 0.2 - - - -
27A ALA 3.0 24.2 + - - -
124A MET* 3.5 9.0 - - - +
125A TYR* 1.3 77.6 - - - +
127A PHE* 1.3 87.8 + - - +
307A PHE* 3.4 16.2 - - - -
308A VAL* 3.7 6.0 - - - +
311A LYS* 4.0 3.8 + - - -
351A GLY* 3.4 4.4 - - - -
352A PRO* 3.3 16.1 - - + -
353A TYR* 2.8 25.0 + - + +
354A PHE* 2.7 42.6 + - + +
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Residues in contact with PHE 127 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A VAL* 5.0 0.4 - - + -
25A LEU 3.0 12.6 - - - +
26A CYS* 4.0 7.0 - - - -
105A PHE* 3.7 33.9 - + + -
124A MET* 4.1 2.0 - - - -
126A ASP* 1.3 82.9 + - - +
128A TYR* 1.3 64.6 + - - +
129A VAL* 4.4 9.0 - - + -
307A PHE* 6.1 0.2 - + - -
308A VAL* 3.8 28.5 - - + -
311A LYS* 2.7 64.5 + - + -
312A MET* 3.7 36.1 - - + -
315A LEU* 4.0 19.3 - - + -
354A PHE* 3.6 7.5 - - - +
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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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17A LEU 5.5 0.2 - - - -
18A ILE* 3.9 40.3 + - + +
23A HIS 4.1 10.8 - - - -
24A VAL* 3.4 13.5 - - - +
25A LEU* 2.7 48.4 + - + -
127A PHE* 1.3 74.5 - - - +
129A VAL* 1.3 72.3 + - - +
130A PRO* 3.7 29.0 - - + +
131A PRO* 4.0 10.0 - - - +
354A PHE* 3.8 20.4 - - + -
355A HIS 3.4 26.5 - - - -
356A GLN* 3.6 15.4 + - - -
357A GLU* 5.1 3.1 - - - +
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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