Contacts of the strand formed by residues 85 - 92 (chain A) in PDB entry 5PJP
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLY* 3.7 2.6 - - - -
82A ARG* 2.9 54.8 + - + +
84A GLY* 1.3 84.4 - - - +
86A PHE* 1.3 57.6 + - - +
230A LEU* 4.0 30.7 - - + +
231A PHE* 3.6 26.7 - - + -
248A LEU 3.5 4.9 - - - +
249A ILE* 4.9 0.7 - - + -
253A VAL* 4.1 26.0 - - + -
411A EDO 4.9 3.2 - - - -
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Residues in contact with PHE 86 (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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79A ALA* 4.0 10.8 - - + -
80A SER 3.2 17.5 - - - +
81A GLY* 4.3 0.2 - - - -
82A ARG 3.4 10.3 - - - +
83A ALA 3.5 26.7 - - - -
84A GLY 4.5 0.2 - - - -
85A VAL* 1.3 76.8 - - - +
87A THR* 1.3 77.4 + - - +
88A GLN* 4.6 5.2 - - - -
125A TYR* 4.0 7.2 - - - -
126A TRP* 3.8 14.1 - + - -
129A ARG* 3.6 36.1 - - + -
130A ILE* 3.6 15.0 - - + -
231A PHE* 3.8 4.5 - - - -
247A ALA* 3.7 1.9 - - - -
248A LEU* 2.8 67.0 + - + +
411A EDO 4.6 0.7 - - - -
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Residues in contact with THR 87 (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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79A ALA* 3.2 4.0 - - - -
80A SER* 2.9 33.3 + - - -
86A PHE* 1.3 83.6 - - - +
88A GLN* 1.3 62.5 + - - +
231A PHE* 3.6 26.5 - - + -
234A SER* 5.4 6.1 - - - +
246A VAL* 3.1 24.2 - - + +
247A ALA* 4.4 4.3 - - + -
411A EDO 2.7 30.3 + - - +
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Residues in contact with GLN 88 (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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77A GLN* 3.3 16.1 - - - +
78A VAL 3.2 11.7 - - - +
79A ALA* 4.5 0.7 - - - -
86A PHE* 4.6 3.5 - - + -
87A THR* 1.3 76.7 - - - +
89A TYR* 1.3 64.6 + - - +
90A HIS* 4.0 10.6 + - - +
129A ARG* 2.9 30.3 + - - +
188A THR* 3.1 46.8 + - - +
190A ALA* 4.2 9.1 - - - +
245A LYS 4.9 2.6 + - - +
246A VAL* 3.0 44.8 + - - +
248A LEU* 4.1 10.1 - - + +
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Residues in contact with TYR 89 (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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76A GLN 3.2 2.4 - - - +
77A GLN* 3.5 2.6 - - - -
78A VAL* 2.9 70.3 + - + +
80A SER* 5.5 6.3 - - - -
88A GLN* 1.3 76.4 - - - +
90A HIS* 1.3 70.4 + - - +
91A LYS* 4.0 30.2 + - + +
246A VAL* 5.2 2.7 - - + -
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Residues in contact with HIS 90 (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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75A LEU* 3.6 38.7 - - + +
76A GLN 3.5 2.7 - - - -
77A GLN* 3.1 43.7 + - + -
88A GLN* 4.0 13.8 + - + +
89A TYR* 1.3 86.4 - - - +
91A LYS* 1.3 60.2 + - - +
92A LYS* 3.8 6.1 + - - +
136A TYR* 6.2 0.4 - + - -
138A ALA* 6.3 1.8 - - + -
245A LYS 5.1 9.6 + - - -
246A VAL* 6.0 2.9 - - + -
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Residues in contact with LYS 91 (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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75A LEU* 3.6 1.9 - - - -
76A GLN* 2.9 64.1 + - + +
78A VAL* 4.5 5.4 - - + -
89A TYR* 3.8 27.4 + - + +
90A HIS* 1.3 71.4 - - - +
92A LYS* 1.3 69.7 + - - +
93A LYS* 3.5 11.2 + - + +
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Residues in contact with LYS 92 (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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73A THR* 3.6 26.5 - - + -
74A PRO 3.7 5.8 - - - -
75A LEU* 4.2 10.1 - - + -
90A HIS 3.8 4.7 + - - +
91A LYS* 1.3 81.9 - - - +
93A LYS* 1.3 64.2 + - - +
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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