Contacts of the strand formed by residues 127 - 135 (chain A) in PDB entry 5JPM
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 ILE 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A PHE* 4.6 5.8 - - + -
59A ARG* 5.0 20.4 - - - +
111A VAL* 3.6 36.3 - - + -
112A ALA 3.4 26.0 - - - +
113A HIS* 3.6 22.4 - - + -
117A LEU* 3.8 2.4 - - - +
123A ARG* 4.8 4.0 + - - +
125A THR* 3.0 35.6 + - + +
126A ASN* 1.3 80.3 - - - +
128A GLN* 1.3 63.1 + - - +
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Residues in contact with GLN 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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23A LEU* 3.0 32.3 + - + +
25A LEU* 4.0 11.4 - - + +
111A VAL* 4.2 3.1 - - - -
112A ALA* 2.6 45.0 + - + +
117A LEU* 3.8 29.4 - - + +
121A LEU* 4.4 5.4 - - - +
123A ARG* 5.9 3.8 - - + +
127A ILE* 1.3 74.9 - - - +
129A GLY* 1.3 57.8 - - - +
655A SER* 3.4 26.2 + - - +
656A ASP 3.9 2.8 - - - +
657A GLY* 3.5 29.0 + - - +
660A TRP* 4.7 9.0 - - + -
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Residues in contact with GLY 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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25A LEU* 4.2 6.5 - - - -
109A GLN* 5.6 2.5 - - - -
110A LEU 3.1 14.8 - - - -
111A VAL* 3.8 12.1 - - - +
128A GLN* 1.3 79.2 - - - +
130A ILE* 1.3 62.7 + - - -
131A ASN* 5.5 0.4 - - - -
655A SER* 4.2 2.5 - - - -
660A TRP* 3.1 24.6 - - - -
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Residues in contact with ILE 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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25A LEU* 4.5 15.0 - - + +
27A SER* 4.9 2.9 - - - -
109A GLN* 3.2 2.2 - - - +
110A LEU* 3.0 45.8 + - + +
129A GLY* 1.3 76.9 - - - +
131A ASN* 1.3 70.6 + - - +
132A LEU* 4.0 19.7 - - + +
653A ALA* 4.3 18.6 - - + +
654A PHE 3.8 2.2 - - - +
655A SER* 3.6 31.6 - - - +
660A TRP* 4.0 9.2 - - + -
661A THR* 3.6 30.1 - - - +
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Residues in contact with ASN 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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29A SER* 4.8 0.3 + - - +
61A PRO* 4.9 8.7 - - - +
107A GLU* 3.1 29.3 + - - +
108A VAL 3.3 5.8 - - - +
109A GLN* 3.2 30.9 + - - +
130A ILE* 1.3 76.6 - - - +
132A LEU* 1.3 70.0 + - - +
653A ALA* 4.4 5.5 - - - +
661A THR* 5.6 1.1 + - - +
663A SER* 3.3 28.1 + - - +
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Residues in contact with LEU 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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27A SER* 3.9 15.7 - - - +
28A PRO 3.4 25.4 - - - +
29A SER 3.3 12.3 - - - +
31A VAL* 4.5 6.3 - - + -
37A LEU* 4.3 12.1 - - + -
58A LEU* 4.5 6.3 - - + -
107A GLU* 3.2 4.0 - - - -
108A VAL* 2.3 60.8 + - + +
110A LEU* 4.0 20.2 - - + +
130A ILE* 4.0 14.6 - - + +
131A ASN* 1.3 78.8 - - - +
133A LEU* 1.3 68.8 + - - +
653A ALA* 3.6 21.8 - - + -
663A SER* 4.3 2.2 - - - -
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Residues in contact with LEU 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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29A SER 3.3 6.2 + - - +
30A VAL* 3.1 15.5 - - + -
31A VAL* 2.9 26.4 + - - +
105A GLY 5.8 0.2 - - - -
106A PRO* 3.2 29.6 - - + +
107A GLU* 4.1 11.2 - - + -
132A LEU* 1.3 77.3 - - - +
134A PHE* 1.3 61.5 + - - +
663A SER* 4.4 7.3 + - - +
664A ARG* 3.5 42.0 - - + +
665A LYS 4.4 3.4 - - - +
666A ARG* 4.1 14.8 - - - +
667A LEU* 3.8 22.7 - - + +
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Residues in contact with PHE 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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30A VAL* 3.9 2.6 - - - +
31A VAL* 3.2 22.2 - - + +
33A LEU* 4.0 31.4 - - + -
99A LEU* 3.4 40.6 - - + -
100A HIS* 5.4 2.5 - - - -
102A LEU* 3.5 19.3 - - + -
105A GLY 4.8 0.4 - - - -
106A PRO* 3.1 44.8 + - + +
107A GLU 3.5 17.5 - - - -
108A VAL* 4.2 9.4 - - + -
133A LEU* 1.3 76.3 - - - +
135A SER* 1.3 65.8 + - - +
136A SER* 5.3 3.6 - - - -
224A GLU* 4.7 2.8 - - - +
667A LEU* 5.0 3.3 - - - +
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Residues in contact with SER 135 (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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30A VAL* 4.1 2.2 - - - +
31A VAL 3.1 5.5 + - - -
32A HIS* 3.4 21.7 + - - -
33A LEU* 3.0 29.2 + - - +
134A PHE* 1.3 78.4 - - - +
136A SER* 1.3 61.2 + - - +
137A ARG* 3.1 19.5 + - - +
224A GLU* 2.7 25.3 + - - -
667A LEU* 3.8 20.5 - - - +
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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