Contacts of the strand formed by residues 107 - 113 (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 GLU 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A PRO* 3.9 19.6 - - + +
99A LEU* 4.8 3.3 - - - +
104A ARG* 5.8 3.5 - - - +
105A GLY* 2.9 24.6 + - - +
106A PRO* 1.3 74.6 - - - +
108A VAL* 1.3 62.3 + - - +
131A ASN* 3.1 30.8 + - + +
132A LEU 3.2 10.3 - - - +
133A LEU* 4.1 11.9 - - + -
134A PHE* 3.5 8.9 - - - -
663A SER* 5.7 1.4 + - - +
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Residues in contact with VAL 108 (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 VAL* 3.8 27.4 - - + -
58A LEU* 3.9 17.7 - - + -
59A ARG 3.2 23.1 - - - +
61A PRO* 4.0 7.0 - - + -
68A CYS* 4.7 0.2 - - - -
99A LEU* 3.7 36.8 - - + -
107A GLU* 1.3 72.4 - - - +
109A GLN* 1.3 65.1 + - - +
131A ASN* 3.3 4.0 - - - +
132A LEU* 2.3 53.4 + - + +
134A PHE* 4.3 8.7 - - + -
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Residues in contact with GLN 109 (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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58A LEU* 3.5 5.8 - - - +
59A ARG* 2.4 83.7 + - + +
61A PRO* 4.1 22.9 - - + +
65A ASN* 4.7 0.2 + - - -
108A VAL* 1.3 77.8 - - - +
110A LEU* 1.3 59.7 + - - +
111A VAL* 3.8 13.2 + - + +
129A GLY 5.9 1.2 - - - -
130A ILE 3.2 8.9 - - - +
131A ASN* 3.2 28.4 + - - +
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Residues in contact with LEU 110 (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* 3.8 12.9 - - + +
27A SER* 3.7 31.6 - - - +
37A LEU* 4.8 1.8 - - + -
39A VAL* 3.7 27.4 - - + -
56A VAL* 3.7 15.9 - - + -
57A PHE 3.6 24.5 - - - +
58A LEU* 3.6 15.6 - - + +
87A LEU* 3.8 20.6 - - + -
108A VAL 4.3 0.4 + - - -
109A GLN* 1.3 70.5 - - - +
111A VAL* 1.3 59.5 + - - +
129A GLY* 3.1 19.2 - - - -
130A ILE* 3.0 15.7 + - + +
132A LEU* 4.0 12.4 - - + +
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Residues in contact with VAL 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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25A LEU* 4.7 0.2 - - - -
55A SER 4.2 0.3 - - - +
56A VAL* 3.3 4.5 - - - +
57A PHE* 2.8 63.4 + - + +
59A ARG* 3.9 18.8 - - + +
109A GLN* 3.8 31.0 - - + +
110A LEU* 1.3 77.7 - - - +
112A ALA* 1.3 60.2 + - - +
113A HIS 4.2 0.2 + - - -
127A ILE* 3.6 30.1 - - + -
128A GLN 3.4 3.4 - - - +
129A GLY* 3.9 12.8 - - - +
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Residues in contact with ALA 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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23A LEU* 4.8 14.1 - - + -
25A LEU* 4.2 15.7 - - + +
41A VAL* 5.9 1.3 - - + -
55A SER 3.3 5.4 - - - +
56A VAL* 3.9 17.3 - - + +
74A PHE* 4.4 13.0 - - + -
111A VAL* 1.3 73.6 - - - +
113A HIS* 1.3 60.3 + - - +
114A SER* 5.5 0.2 - - - -
117A LEU* 3.8 7.0 - - - +
127A ILE* 3.4 3.6 - - - +
128A GLN* 2.6 38.5 + - + +
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Residues in contact with HIS 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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54A GLY* 3.2 2.6 - - - -
55A SER* 2.5 45.0 + - - +
57A PHE* 4.2 15.7 - + + -
74A PHE* 4.3 0.8 - - - -
111A VAL 4.2 0.2 - - - -
112A ALA* 1.3 72.3 - - - +
114A SER* 1.3 62.2 + - - +
115A PRO* 5.0 6.8 - - + +
126A ASN* 3.0 44.2 + - + +
127A ILE* 3.6 19.0 - - + +
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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