Contacts of the strand formed by residues 55 - 67 (chain A) in PDB entry 2JGB
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 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A PRO* 3.9 21.8 - - + -
53A GLU 3.5 9.6 - - - +
54A HIS* 1.3 85.5 - - + +
56A LEU* 1.3 62.6 + - - +
89A ALA 3.9 6.7 - - - +
52B ILE* 3.5 23.5 - - + +
54B TYR* 2.6 34.4 + - - +
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Residues in contact with LEU 56 (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 PRO* 1.3 79.0 - - - +
57A GLN* 1.3 65.7 + - - +
58A TYR* 3.3 22.5 + - - +
59A ASN* 5.7 0.2 - - - +
60A TYR* 4.4 5.6 - - + -
88A PHE* 3.6 38.4 - - + -
89A ALA 3.2 10.6 + - - +
90A SER 3.7 21.8 - - - +
91A VAL* 3.9 22.9 - - + -
156A LEU* 3.7 36.3 - - + +
52B ILE* 3.9 9.8 - - - +
54B TYR* 4.1 9.2 - - + -
59B LEU* 5.2 1.1 - - + -
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Residues in contact with GLN 57 (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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56A LEU* 1.3 75.1 - - - +
58A TYR* 1.3 88.9 + - + +
156A LEU 5.0 2.8 + - - +
158A GLU* 3.6 26.9 - - + +
164A GLU* 5.1 1.4 + - - -
51B ARG* 3.4 39.9 - - - +
52B ILE* 2.7 44.4 + - - +
54B TYR* 5.6 0.2 - - - -
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Residues in contact with TYR 58 (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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56A LEU* 3.3 23.4 - - - +
57A GLN* 1.3 94.5 + - + +
59A ASN* 1.3 73.4 + - - +
60A TYR* 3.3 24.6 - - + -
89A ALA 5.0 0.2 - - - +
117A LYS* 3.6 41.7 + - + -
158A GLU* 3.2 27.6 - - - -
163A GLY 3.6 5.5 + - - -
164A GLU* 2.7 33.6 + - - -
51B ARG* 3.0 20.4 + - - -
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Residues in contact with ASN 59 (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 VAL* 3.0 32.2 + - - +
58A TYR* 1.3 78.6 - - - +
60A TYR* 1.3 60.7 + - - +
87A THR* 4.6 1.5 - - + +
88A PHE 3.3 13.2 - - - +
89A ALA* 3.2 21.2 - - - +
117A LYS* 3.6 6.2 - - - +
118A GLU* 2.8 53.6 + - + +
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Residues in contact with TYR 60 (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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56A LEU* 4.4 4.7 - - + -
57A GLN* 6.2 0.2 - - + -
58A TYR* 3.3 37.9 - + + -
59A ASN* 1.3 73.3 - - - +
61A THR* 1.3 63.3 + - - +
87A THR* 3.3 5.4 - - - +
88A PHE* 2.9 58.2 + + + -
115A LEU* 3.8 5.8 - - + -
116A PHE 3.4 21.5 - - - +
117A LYS* 3.7 18.5 - - + +
118A GLU 3.9 0.9 - - - +
155A MET* 3.6 49.8 + - + +
156A LEU* 3.4 32.7 + - + -
158A GLU* 3.8 12.6 + - - -
166A ILE* 5.7 0.6 - - + +
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Residues in contact with THR 61 (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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60A TYR* 1.3 74.3 - - - +
62A PHE* 1.3 72.5 + - - +
63A TRP* 3.3 27.7 - - + +
84A GLN* 3.7 28.5 + - + +
86A GLY 3.4 10.3 - - - +
87A THR* 2.9 20.4 + - - +
115A LEU* 3.4 5.8 - - - +
116A PHE 2.8 33.6 + - - -
117A LYS 5.3 0.2 - - - -
118A GLU* 3.9 16.6 - - - +
119A GLY 5.1 0.6 + - - -
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Residues in contact with PHE 62 (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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60A TYR 4.4 0.2 - - - -
61A THR* 1.3 79.8 - - - +
63A TRP* 1.3 56.0 + - - +
84A GLN* 3.6 0.5 - - - -
85A ILE* 2.8 48.0 + - + -
86A GLY 2.9 11.4 + - - +
88A PHE* 3.7 28.7 - + - -
94A PHE* 3.9 26.2 - + - -
97A PHE* 4.1 27.1 - + + -
98A TYR* 4.3 9.2 - + + -
101A MET* 4.0 31.4 - - + -
113A PHE* 5.3 1.3 - - + -
114A HIS 3.4 9.9 - - - -
115A LEU* 3.8 23.9 - - + +
148A TRP* 4.3 17.0 - + - -
152A ILE* 4.5 2.9 - - + -
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Residues in contact with TRP 63 (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 THR* 3.3 35.9 + - + +
62A PHE* 1.3 75.6 - - - +
64A TYR* 1.3 62.5 + - - +
79A GLU* 6.1 1.8 - - + -
82A ILE* 3.8 31.2 - - + -
83A LYS 3.1 7.2 - - - +
84A GLN* 3.5 46.0 - - + -
85A ILE* 4.3 3.0 - - - +
113A PHE* 3.4 9.7 - - - +
114A HIS* 2.8 50.1 + - + +
116A PHE* 4.3 5.6 - - + +
117A LYS 5.8 0.2 + - - -
119A GLY 6.3 0.7 - - - -
120A ILE 4.2 9.8 + - - -
121A LYS* 4.1 29.6 - - + -
122A PRO* 3.5 33.0 - - + +
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Residues in contact with TYR 64 (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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63A TRP* 1.3 76.9 - - - +
65A SER* 1.3 78.6 + - - +
66A ARG* 3.4 42.0 + - + +
81A ASN 4.0 0.5 - - - +
82A ILE* 3.5 2.7 - - - -
83A LYS* 2.9 60.4 + - + +
85A ILE* 3.8 21.3 - - + -
107A LEU* 4.2 21.2 - - + +
111A SER* 4.1 8.4 + - - -
112A ASP 3.4 13.5 - - - -
113A PHE* 3.8 16.2 - + + -
114A HIS* 4.4 0.4 - - - -
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Residues in contact with SER 65 (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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64A TYR* 1.3 82.7 - - - +
66A ARG* 1.3 61.8 + - - +
67A ARG* 2.8 34.1 + - - -
81A ASN 3.4 17.3 - - - -
82A ILE* 4.1 5.2 - - - -
111A SER* 3.2 5.5 - - - -
112A ASP* 2.9 40.5 + - - +
114A HIS* 3.0 17.9 + - - -
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Residues in contact with ARG 66 (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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64A TYR* 3.4 29.9 + - + +
65A SER* 1.3 76.4 - - - +
67A ARG* 1.3 64.8 + - - +
71A ARG* 5.0 0.3 + - - -
81A ASN* 2.6 30.0 + - - +
107A LEU* 6.4 0.2 - - - +
108A THR* 2.7 44.0 + - - +
109A GLY* 3.9 10.5 - - - +
110A HIS 3.4 8.5 - - - +
111A SER* 3.4 13.0 - - - +
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Residues in contact with ARG 67 (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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65A SER* 2.8 31.4 + - - -
66A ARG* 1.3 79.5 - - - +
68A THR* 1.3 73.1 + - - +
71A ARG* 3.5 29.4 - - - +
73A THR* 6.0 1.3 - - - -
78A TYR* 3.0 52.6 + - - +
81A ASN* 3.0 39.2 + - - +
82A ILE* 4.5 0.6 - - - +
110A HIS* 2.9 44.6 + - + +
112A ASP* 4.8 5.4 + - - +
114A HIS* 4.6 1.2 - - - -
1000B MGT 3.6 30.0 + - - +
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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