Contacts of the strand formed by residues 69 - 79 (chain A) in PDB entry 5JSJ
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 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLY* 3.8 12.3 - - - -
62A TRP 3.2 23.3 - - - +
63A LYS* 4.4 22.2 - - + +
68A PRO* 1.3 77.7 - - + +
70A THR* 1.3 66.1 + - - +
71A GLN* 5.6 1.1 - - - +
109A SER* 4.1 11.9 - - - +
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Residues in contact with THR 70 (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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61A GLY* 3.2 5.9 - - - -
62A TRP* 2.8 43.1 + - - +
68A PRO* 4.2 15.3 - - + +
69A VAL* 1.3 80.0 - - - +
71A GLN* 1.3 60.9 + - - +
72A TRP* 2.8 35.1 + - + -
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Residues in contact with GLN 71 (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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59A GLN* 3.3 43.9 + - - +
60A HIS* 3.7 18.7 - - - +
61A GLY* 4.0 5.0 + - - -
69A VAL* 5.6 1.4 - - - +
70A THR* 1.3 73.1 - - - +
72A TRP* 1.3 71.2 + - - +
73A LYS* 6.0 1.3 - - + -
110A ALA* 5.5 4.6 + - - +
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Residues in contact with TRP 72 (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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59A GLN* 3.1 29.0 - - - +
60A HIS* 3.1 16.6 + + - +
62A TRP* 3.7 22.2 - + + +
64A GLU* 6.1 1.1 - - - -
70A THR* 2.8 38.3 + - + -
71A GLN* 1.3 82.8 + - - +
73A LYS* 1.3 63.1 + - - +
91A TYR* 3.8 29.6 - + + -
92A ASP 5.6 1.1 - - - -
94A PHE* 3.7 29.4 - + - -
301A 6PD 3.7 56.3 - + + -
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Residues in contact with LYS 73 (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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57A ARG* 3.6 19.9 - - - +
58A ILE* 3.3 8.5 - - - +
59A GLN* 4.0 24.9 - - + +
60A HIS* 6.4 0.2 - - - -
71A GLN* 6.0 1.1 - - + -
72A TRP* 1.3 77.5 - - - +
74A GLY* 1.3 59.5 + - - +
91A TYR* 3.5 11.4 - - - +
92A ASP* 3.0 40.5 + - + +
114A LEU* 4.3 13.4 - - + +
116A ASP* 5.7 1.6 + - - -
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Residues in contact with GLY 74 (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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57A ARG* 3.2 9.3 + - - +
58A ILE* 2.9 41.2 + - - +
73A LYS* 1.3 76.4 - - - +
75A THR* 1.3 63.3 + - - -
89A ILE* 4.2 7.9 - - - -
90A LYS 3.2 13.7 - - - -
91A TYR* 4.0 4.5 - - - -
92A ASP* 3.9 5.1 + - - -
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Residues in contact with THR 75 (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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55A GLY 4.9 0.4 - - - +
56A CYS 3.7 8.3 - - - +
57A ARG* 3.2 27.3 + - - +
74A GLY* 1.3 71.4 - - - -
76A VAL* 1.3 66.8 + - - +
77A LEU* 3.4 7.0 + - + +
89A ILE* 3.5 3.5 - - - -
90A LYS* 2.9 34.9 + - - -
92A ASP* 4.7 0.3 + - - -
118A VAL* 4.2 14.5 - - + +
161A VAL* 4.0 26.9 - - + -
162A MET* 4.2 23.5 - - - -
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Residues in contact with VAL 76 (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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53A ILE* 3.2 35.9 - - + +
54A VAL* 3.8 10.3 - - - -
55A GLY* 3.0 26.3 + - - -
56A CYS 2.9 16.5 + - - +
58A ILE* 3.9 33.4 - - + -
75A THR* 1.3 72.4 - - - +
77A LEU* 1.3 60.1 + - - +
78A ASP 4.0 16.8 - - - +
87A TYR* 4.1 14.6 - - + -
88A LEU 3.8 5.2 - - - +
89A ILE* 4.6 3.8 - - + +
102A LEU* 4.4 5.2 - - + -
161A VAL* 3.8 2.4 - - - +
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Residues in contact with LEU 77 (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 VAL* 3.8 6.5 - - - +
75A THR* 3.8 14.6 - - + +
76A VAL* 1.3 74.1 - - - +
78A ASP* 1.3 63.4 + - - +
88A LEU* 2.8 11.6 + - + +
89A ILE 4.1 0.9 - - - -
90A LYS* 3.9 15.9 - - + +
97A VAL* 4.0 22.4 - - + -
160A PRO* 3.6 32.4 - - + +
161A VAL* 3.5 21.4 - - + +
162A MET* 4.0 27.8 - - + -
167A TYR* 4.2 16.6 - - + +
178A MET* 3.7 29.2 - - + -
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Residues in contact with ASP 78 (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 VAL* 3.7 14.3 - - - +
76A VAL* 3.6 2.5 - - - +
77A LEU* 1.3 82.3 - - + +
79A GLN* 1.3 89.0 + - - +
80A VAL* 4.2 1.8 - - - +
81A PRO* 4.8 7.0 - - - +
87A TYR* 3.4 9.9 - - - +
88A LEU* 2.9 46.9 + - + +
160A PRO* 4.9 11.2 - - + +
167A TYR* 5.2 0.9 - - - +
234A HIS* 5.8 2.4 + - - -
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Residues in contact with GLN 79 (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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52A ASN* 3.9 17.0 - - - +
53A ILE 5.6 0.2 + - - -
54A VAL* 3.5 14.5 - - + +
78A ASP* 1.3 87.1 + - - +
80A VAL* 1.3 66.0 + - - +
81A PRO* 3.2 12.0 - - - +
84A PRO* 2.7 45.1 + - + +
86A LEU 3.7 3.1 - - - +
87A TYR* 3.2 31.0 + - + -
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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