Contacts of the helix formed by residues 90 - 104 (chain A) in PDB entry 5JJA
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 PRO 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A GLU* 3.9 22.9 - - - +
43A ILE* 4.3 13.8 - - + +
88A THR* 3.5 14.1 - - - +
89A GLU* 1.3 95.2 - - + +
91A ILE* 1.3 60.1 + - - +
92A TYR 3.4 0.2 - - - -
93A PRO* 3.5 11.2 - - + +
94A GLU* 3.4 20.6 - - - +
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Residues in contact with ILE 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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39A GLU* 4.2 13.0 - - + -
42A PHE* 3.4 38.8 - - + -
43A ILE* 3.8 25.1 - - + -
46A LEU* 4.4 4.0 - - + -
86A VAL 3.8 7.4 - - - +
87A ILE* 4.5 14.4 - - + -
88A THR* 3.0 34.4 + - - +
90A PRO* 1.3 76.8 - - - +
92A TYR* 1.3 65.8 + - - +
94A GLU* 3.1 7.0 + - - +
95A VAL* 2.9 41.5 + - + +
144A PHE* 4.6 1.6 - - + -
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Residues in contact with TYR 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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87A ILE* 3.7 17.4 + - + +
88A THR 3.3 31.4 - - - -
89A GLU* 3.7 9.2 - - - +
91A ILE* 1.3 78.2 - - - +
93A PRO* 1.4 70.6 - - + +
95A VAL* 3.4 1.9 + - - +
96A VAL* 3.1 30.5 + - + +
144A PHE* 3.6 23.5 - + - -
149A ASP 3.5 10.2 + - - -
150A PHE* 3.6 15.9 - + - -
151A GLN* 2.8 36.6 + - - +
154A ILE* 3.8 20.9 - - + -
155A ALA* 3.8 33.0 - - + -
158A TYR* 3.9 15.9 - - + -
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Residues in contact with PRO 93 (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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89A GLU 3.5 9.6 - - - +
90A PRO* 3.5 16.8 - - + +
92A TYR* 1.4 95.2 - - + +
94A GLU* 1.3 62.6 - - + +
96A VAL* 4.1 2.3 - - + +
97A HIS* 2.9 32.1 + - - +
158A TYR* 3.7 40.8 - - + +
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Residues in contact with GLU 94 (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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43A ILE* 4.0 19.3 - - + +
46A LEU* 3.7 24.9 - - + +
47A ARG* 2.9 51.6 + - - +
50A CYS* 5.5 0.5 - - - -
90A PRO 3.4 19.3 - - - +
91A ILE 3.1 5.8 + - - +
93A PRO* 1.3 78.6 - - + +
95A VAL* 1.3 61.4 + - - +
97A HIS* 4.0 8.9 + - - +
98A MET* 3.0 29.8 + - - +
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Residues in contact with VAL 95 (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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46A LEU* 3.9 12.1 - - + -
91A ILE* 2.9 38.5 + - + +
92A TYR 3.8 4.0 - - - +
94A GLU* 1.3 76.1 - - - +
96A VAL* 1.3 57.7 + - - +
98A MET* 3.3 7.9 + - + +
99A PHE* 2.9 27.0 + - - +
140A PHE* 3.8 28.9 - - + -
141A PHE* 3.9 13.7 - - + -
144A PHE* 3.6 42.8 - - + -
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Residues in contact with VAL 96 (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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92A TYR* 3.1 19.9 + - + +
93A PRO 4.1 2.7 - - - +
95A VAL* 1.3 74.0 - - - +
97A HIS* 1.3 60.4 + - - +
99A PHE* 3.4 7.1 + - - +
100A ALA* 3.0 29.1 + - + +
141A PHE* 4.5 9.6 - - + -
144A PHE* 4.8 6.1 - - + -
155A ALA* 6.4 0.7 - - + -
158A TYR* 3.9 33.2 - - + +
159A ILE* 4.0 21.3 - - + -
163A PHE* 3.9 25.5 - - + -
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Residues in contact with HIS 97 (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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47A ARG* 6.2 1.2 - - - +
50A CYS* 3.7 26.3 - - + -
93A PRO 2.9 20.5 + - - +
94A GLU* 4.0 8.6 + - - +
96A VAL* 1.3 76.2 - - - +
98A MET* 1.3 62.6 + - - +
100A ALA* 3.3 7.7 + - + +
101A VAL* 3.0 44.6 + - + +
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Residues in contact with MET 98 (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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46A LEU* 3.4 48.2 - - + +
49A CYS* 4.1 9.0 - - + -
50A CYS* 3.8 12.8 - - - -
73A LEU* 4.0 20.4 - - + -
76A MET* 4.3 4.0 - - + -
94A GLU 3.0 20.7 + - - +
95A VAL* 3.6 4.5 - - + +
97A HIS* 1.3 78.1 + - - +
99A PHE* 1.3 64.4 + - + +
101A VAL* 3.5 0.9 + - - -
102A ASN* 2.9 45.7 + - - +
137A VAL* 4.1 21.3 - - + -
140A PHE* 4.1 18.4 - - + -
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Residues in contact with PHE 99 (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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95A VAL 2.9 17.8 + - - +
96A VAL* 3.6 5.4 - - - +
98A MET* 1.3 78.0 - - + +
100A ALA* 1.3 60.0 + - - +
102A ASN* 3.2 2.4 + - - -
103A MET* 2.8 60.9 + - + +
104A PHE* 4.0 6.5 - + - -
137A VAL* 3.9 20.0 - - + -
138A TYR* 4.0 23.8 - + - -
141A PHE* 3.5 48.2 - + + -
163A PHE* 3.6 22.2 - + - -
167A LEU* 3.8 31.6 - - + -
170A LEU* 5.5 0.2 - - + -
185A THR* 5.2 1.6 - - + -
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Residues in contact with ALA 100 (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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96A VAL* 3.0 18.8 + - + +
97A HIS* 3.3 9.2 + - + +
99A PHE* 1.3 76.1 - - - +
101A VAL* 1.3 61.5 + - + +
104A PHE* 2.9 68.1 + - + +
163A PHE* 5.1 2.5 - - + -
374B LEU* 3.9 7.4 - - + +
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Residues in contact with VAL 101 (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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50A CYS* 3.6 37.9 - - + +
52A LEU* 3.5 27.3 - - + +
97A HIS* 3.0 43.8 + - + +
98A MET 4.1 1.6 - - - +
100A ALA* 1.3 78.7 - - + +
102A ASN* 1.3 62.4 + - - +
104A PHE 4.7 3.1 - - - +
105A ARG* 6.0 0.5 - - - +
374B LEU* 4.0 21.0 - - + +
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Residues in contact with ASN 102 (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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49A CYS 3.0 21.4 + - - -
50A CYS* 4.3 3.4 - - - +
52A LEU* 3.6 15.4 - - - +
69A LYS* 2.8 26.8 + - - -
98A MET* 2.9 38.1 + - - +
99A PHE 3.8 2.9 - - - +
101A VAL* 1.3 78.9 - - - +
103A MET* 1.3 59.5 + - - +
104A PHE 5.4 0.2 - - - -
105A ARG* 3.9 12.4 - - - +
133A HIS* 5.3 1.9 - - - +
134A LEU* 3.6 24.3 - - + +
137A VAL* 4.0 26.0 - - + +
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Residues in contact with MET 103 (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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99A PHE* 2.8 46.3 + - + +
102A ASN* 1.3 79.1 - - - +
104A PHE* 1.3 63.1 + - + +
105A ARG* 2.9 36.9 + - - +
134A LEU* 3.2 48.2 - - + +
137A VAL* 3.5 22.2 - - + -
138A TYR* 3.4 39.9 - - + -
170A LEU* 3.4 15.2 - - + +
178A GLU* 4.2 0.4 - - - +
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Residues in contact with PHE 104 (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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99A PHE* 4.0 16.6 - + - -
100A ALA* 2.9 44.5 + - + +
101A VAL 4.7 3.5 - - - +
103A MET* 1.3 71.9 - - + +
105A ARG* 1.3 59.4 + - - +
163A PHE* 3.7 46.9 - + - -
166A GLN* 3.6 45.1 - - + +
167A LEU* 3.6 22.2 - - - -
170A LEU* 4.1 7.9 - - + -
374B LEU* 3.5 33.4 - - + +
375B TYR* 3.7 17.9 - - - +
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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