Contacts of the strand formed by residues 104 - 124 (chain A) in PDB entry 2V72
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 LYS 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ALA* 3.6 0.5 - - - -
65A ILE* 2.8 51.5 + - + +
67A PRO* 3.7 8.6 - - + +
75A PHE* 5.8 1.0 - - - +
76A ILE 5.5 1.8 + - - -
97A TRP* 3.6 59.3 - - + +
98A GLU* 3.6 20.7 + - - +
100A ASN* 2.9 42.2 + - - +
102A LEU* 3.0 20.4 + - - +
103A VAL* 1.3 74.3 - - - +
105A THR* 1.3 60.9 + - - +
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Residues in contact with THR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A SER* 5.9 2.7 - - - -
63A ILE 3.4 7.9 - - - +
64A ALA* 4.4 7.0 - - + -
97A TRP* 4.7 4.9 + - - -
103A VAL* 4.0 17.5 + - + +
104A LYS* 1.3 75.7 - - - +
106A VAL* 1.3 67.0 + - - +
107A THR* 4.3 10.0 + - - -
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A SER* 3.1 5.0 - - - -
63A ILE* 2.8 41.5 + - + +
65A ILE* 4.4 2.5 - - + -
79A TYR* 4.2 14.1 - - + +
81A ILE* 3.9 23.8 - - + -
93A ALA* 3.9 15.5 - - + -
97A TRP* 4.1 19.5 - - + +
105A THR* 1.3 80.1 - - - +
107A THR* 1.3 64.7 + - - +
108A PHE* 3.8 30.3 - - + -
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Residues in contact with THR 107 (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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3A GLU* 5.6 1.3 - - - +
61A SER* 3.3 12.8 - - - +
62A SER* 3.7 10.6 - - - -
105A THR* 4.8 7.3 + - - -
106A VAL* 1.3 80.9 + - - +
108A PHE* 1.3 78.1 + - - +
109A ASP* 3.9 13.4 + - - +
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Residues in contact with PHE 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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60A VAL* 3.7 24.0 - - + +
61A SER* 2.7 30.0 + - - +
62A SER* 4.5 0.2 - - - -
63A ILE* 3.7 29.8 - - + -
81A ILE* 4.9 0.4 - - + -
92A VAL* 3.3 57.2 - - + -
93A ALA* 4.3 2.2 - - + -
106A VAL* 3.8 26.5 - - + -
107A THR* 1.3 76.3 - - - +
109A ASP* 1.3 66.7 + - - +
110A SER 3.2 21.7 + - - +
111A PRO* 3.7 3.2 - - + +
112A ILE* 3.8 15.9 - - + -
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Residues in contact with ASP 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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107A THR* 3.9 13.2 + - - +
108A PHE* 1.3 71.6 - - - +
110A SER* 1.3 58.5 + - - +
111A PRO* 3.5 8.7 - - - +
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Residues in contact with SER 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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108A PHE* 3.3 15.5 - - - +
109A ASP* 1.3 77.1 - - - +
111A PRO* 1.4 71.0 - - - +
112A ILE* 3.5 8.0 + - - +
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Residues in contact with PRO 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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59A LYS* 4.2 26.2 + - + +
60A VAL 3.4 14.8 - - - +
61A SER* 4.4 10.3 - - - -
108A PHE 3.7 6.9 - - - +
109A ASP 3.5 8.5 - - - +
110A SER* 1.4 85.7 - - - +
112A ILE* 1.3 61.6 + - - +
113A ASP* 3.9 5.4 + - - +
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Residues in contact with ILE 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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58A ARG 3.4 0.7 - - - +
59A LYS* 3.3 2.8 - - - -
60A VAL* 2.7 58.3 + - + +
63A ILE* 5.6 1.3 - - + -
81A ILE* 6.2 0.2 - - + -
83A ALA* 4.0 17.5 - - + -
92A VAL* 3.7 47.1 - - + -
108A PHE* 3.8 21.1 - - + -
110A SER 3.8 13.0 - - - +
111A PRO* 1.3 73.2 - - - +
113A ASP* 1.3 65.2 + - - +
114A ALA* 3.5 3.6 + - + -
117A ILE* 5.9 2.5 - - + -
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Residues in contact with ASP 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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57A ALA* 6.4 0.9 - - + -
58A ARG 3.2 6.8 - - - +
59A LYS* 2.8 39.2 + - - +
83A ALA* 4.4 6.2 - - - +
85A ASN* 3.4 36.0 - - - +
90A THR* 6.0 0.9 - - - +
111A PRO 4.9 3.6 - - - +
112A ILE* 1.3 73.5 - - - +
114A ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 114 (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 LEU* 3.3 19.7 - - + +
58A ARG* 2.9 29.9 + - - +
60A VAL* 4.5 6.7 - - + -
83A ALA* 3.7 24.2 - - + -
84A ILE 3.6 5.4 - - - -
85A ASN* 3.7 4.9 + - - -
112A ILE* 3.5 8.7 + - + +
113A ASP* 1.3 75.9 - - - +
115A GLU* 1.3 61.3 + - - +
116A GLU 3.8 10.5 - - - +
117A ILE* 4.6 3.6 - - + -
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Residues in contact with GLU 115 (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 ASN* 3.7 10.4 + - - +
54A LEU* 2.7 34.6 + - - +
55A GLY 4.1 2.0 + - - -
56A LYS* 3.5 18.2 - - - +
57A ALA* 4.7 8.7 - - + +
84A ILE* 2.8 17.6 + - - +
85A ASN* 3.1 20.0 + - - +
86A ASN* 2.7 29.8 + - - -
87A GLY* 3.6 8.9 - - - -
114A ALA* 1.3 72.4 - - - +
116A GLU* 1.3 56.6 + - + +
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Residues in contact with GLU 116 (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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51A SER* 3.8 19.3 + - - -
52A VAL 3.3 22.9 - - - +
53A ASN* 2.8 31.9 + - - +
54A LEU* 4.0 1.5 - - - +
83A ALA* 3.5 4.2 - - - -
84A ILE* 2.9 58.1 + - + +
114A ALA* 3.4 3.2 - - - +
115A GLU* 1.3 83.5 - - + +
117A ILE* 1.3 69.4 + - - +
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Residues in contact with ILE 117 (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 LEU 3.8 0.9 - - - +
51A SER* 3.4 1.9 - - - -
52A VAL* 2.8 44.7 + - + +
54A LEU* 3.9 15.9 - - + -
60A VAL* 4.5 7.2 - - + -
63A ILE* 4.0 17.3 - - + -
81A ILE* 3.6 27.8 - - + -
82A HIS 3.5 6.1 - - - +
83A ALA* 5.2 2.5 - - + -
84A ILE* 4.7 0.9 - - - -
112A ILE* 5.9 1.6 - - + -
114A ALA* 4.6 7.2 - - + -
116A GLU* 1.3 81.1 - - - +
118A LYS* 1.3 63.3 + - - +
119A ILE* 3.8 14.7 - - + +
134A LEU* 5.7 3.4 - - + -
136A VAL* 3.6 41.3 - - + -
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Residues in contact with LYS 118 (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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16A THR* 5.6 2.8 - - - +
49A SER* 3.3 30.1 - - - -
50A LEU 3.4 5.4 - - - +
51A SER* 3.4 21.3 - - - +
80A GLU 3.6 1.4 - - - +
81A ILE* 3.4 7.4 - - - +
82A HIS* 2.9 47.9 + - + +
84A ILE* 4.6 8.3 - - + -
89A GLU* 4.1 22.0 + - - +
117A ILE* 1.3 74.8 - - - +
119A ILE* 1.3 63.0 + - - +
120A THR* 3.8 11.9 + - - +
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Residues in contact with ILE 119 (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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36A TRP* 5.2 2.3 - - - -
49A SER* 3.1 2.7 - - - -
50A LEU* 2.8 43.5 + - + +
52A VAL* 6.0 0.7 - - + -
63A ILE* 4.9 6.1 - - + -
65A ILE* 5.1 3.1 - - + -
76A ILE* 4.7 9.0 - - + -
79A TYR* 4.9 2.5 - - + -
80A GLU 3.7 5.6 - - - +
81A ILE* 3.7 28.7 - - + -
97A TRP* 4.6 20.2 - - + -
117A ILE* 3.8 18.4 - - + +
118A LYS* 1.3 77.0 - - - +
120A THR* 1.3 67.9 + - - +
121A ALA 4.0 0.7 + - - -
131A ILE* 4.3 20.6 - - + -
134A LEU* 3.7 29.2 - - + -
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Residues in contact with THR 120 (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 PRO* 3.8 27.1 - - + -
48A GLN 3.7 7.2 - - - +
49A SER* 3.5 15.8 - - - -
79A TYR* 3.2 10.9 - - - +
80A GLU* 3.0 48.1 + - - +
82A HIS* 4.6 7.3 + - - -
118A LYS* 3.8 13.7 + - - +
119A ILE* 1.3 74.6 - - - +
121A ALA* 1.3 63.0 + - - +
122A ILE* 3.6 8.2 + - + -
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Residues in contact with ALA 121 (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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36A TRP* 5.3 1.1 - - + -
46A LEU* 3.6 8.6 - - + +
47A PRO* 3.1 22.8 - - - +
48A GLN 2.8 15.6 + - - +
76A ILE* 3.8 25.6 - - + -
78A LYS 3.8 4.5 - - - -
119A ILE 4.0 1.6 + - - -
120A THR* 1.3 70.2 - - - +
122A ILE* 1.3 63.6 + - - +
123A GLN 3.5 3.1 - - - +
129A ALA* 3.5 32.1 - - + -
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Residues in contact with ILE 122 (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 19.8 - - - +
47A PRO* 4.3 13.6 - - + +
78A LYS* 2.8 46.6 + - + +
79A TYR 4.0 15.0 - - - +
80A GLU* 3.9 30.7 - - + +
120A THR* 4.5 15.3 - - + +
121A ALA* 1.3 74.1 - - - +
123A GLN* 1.3 68.6 + - + +
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Residues in contact with GLN 123 (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* 3.8 7.4 - - - -
76A ILE* 3.6 6.1 - - - +
77A THR* 2.9 36.5 + - - +
78A LYS* 3.3 32.9 + - + +
121A ALA* 4.7 1.3 - - - +
122A ILE* 1.3 91.4 + - + +
124A GLY* 1.3 57.5 + - - +
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Residues in contact with GLY 124 (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 5.5 - - - +
75A PHE 3.1 15.0 - - - -
76A ILE* 4.1 1.6 - - - -
77A THR* 3.7 6.2 + - - -
121A ALA* 6.0 0.2 - - - -
123A GLN* 1.3 75.2 - - - +
125A VAL* 1.3 66.0 + - - -
126A GLY 3.5 0.2 + - - -
127A GLY* 3.1 16.3 + - - -
128A PHE 3.4 16.8 - - - -
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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
------------------------------------------------------------
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