Contacts of the strand formed by residues 124 - 137 (chain A) in PDB entry 5W6V
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 ARG 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A PRO* 3.3 29.9 - - - +
64A CYS* 4.0 12.7 - - - -
68A VAL* 4.8 5.9 - - - +
116A THR* 3.3 1.9 - - - -
117A ILE* 2.8 38.9 + - + +
122A LYS 3.7 2.4 + - - +
123A ASP* 1.3 76.9 - - - +
125A ILE* 1.3 71.1 + - - +
126A PHE* 3.5 45.5 - - + -
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Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A PRO* 4.5 7.6 - - - +
114A GLU* 5.6 6.7 - - + -
115A VAL 3.3 12.6 - - - +
116A THR* 4.3 14.1 - - - +
123A ASP* 5.5 2.7 - - + +
124A ARG* 1.3 81.9 + - - +
126A PHE* 1.3 73.5 + - - +
127A LYS* 5.4 9.4 - - + +
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Residues in contact with PHE 126 (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 ILE* 4.1 15.7 - - + -
60A LYS 3.7 2.2 - - - +
61A PRO* 3.9 15.7 - - + -
64A CYS* 4.0 17.7 - - - -
68A VAL* 4.0 17.7 - - + -
72A VAL* 4.1 21.8 - - + -
114A GLU* 3.8 2.9 - - - -
115A VAL* 2.6 39.5 + - + +
117A ILE* 3.5 33.2 - - + -
124A ARG* 3.5 60.8 - - + -
125A ILE* 1.3 77.4 - - - +
127A LYS* 1.3 66.1 + - - +
128A VAL* 4.1 2.7 - - + -
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Residues in contact with LYS 127 (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 ASP 3.8 0.7 - - - +
59A ILE* 3.6 1.4 - - - -
60A LYS* 2.8 57.0 + - + +
113A PHE 3.5 7.9 - - - +
114A GLU* 5.3 13.7 - - + -
125A ILE* 5.4 9.9 - - + +
126A PHE* 1.3 76.9 - - - +
128A VAL* 1.3 61.4 + - - +
129A SER* 5.3 1.1 - - - -
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Residues in contact with VAL 128 (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 VAL* 4.0 19.7 - - + -
58A ASP 3.2 8.5 - - - +
59A ILE* 4.3 8.1 - - + -
72A VAL* 3.5 30.7 - - + -
73A VAL* 5.4 0.7 - - + -
76A MET* 4.0 23.3 - - + -
111A VAL 3.8 0.6 - - - +
112A ASP* 3.3 4.3 - - - +
113A PHE* 2.7 47.0 + - + -
115A VAL* 3.9 16.8 - - + -
126A PHE* 4.5 1.1 - - + -
127A LYS* 1.3 82.4 - - - +
129A SER* 1.3 69.3 + - - +
130A ILE* 4.8 0.4 - - + -
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Residues in contact with SER 129 (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 GLU 3.8 0.5 - - - +
57A VAL* 3.4 5.5 - - - +
58A ASP* 2.7 50.7 + - - +
60A LYS* 6.2 0.3 - - - -
110A ARG* 3.7 21.9 + - - -
111A VAL 3.4 5.2 - - - -
112A ASP* 2.8 23.2 + - - -
127A LYS 5.3 1.2 + - - -
128A VAL* 1.3 74.5 + - - +
130A ILE* 1.3 65.4 + - - +
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Residues in contact with ILE 130 (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 TYR* 3.8 32.5 - - + -
56A GLU 3.4 6.3 - - - +
57A VAL* 4.8 6.1 - - + -
76A MET* 3.6 31.0 - - + -
84A ILE* 6.4 0.2 - - + -
85A PHE* 4.1 16.2 - - + -
98A ILE* 5.2 8.3 - - + -
104A LEU* 4.8 11.2 - - + -
106A ILE* 4.8 8.9 - - + +
109A GLU 4.3 1.0 - - - +
110A ARG* 3.4 4.6 - - - -
111A VAL* 2.9 39.0 + - + +
113A PHE* 3.9 22.2 - - + -
128A VAL* 4.8 2.2 - - + -
129A SER* 1.3 79.0 - - - +
131A LYS* 1.3 64.3 + - - +
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Residues in contact with LYS 131 (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 TYR* 3.5 6.2 - - - -
56A GLU* 2.9 42.6 + - + +
106A ILE* 6.2 0.4 - - - -
108A ASN 3.4 24.7 - - - +
109A GLU* 4.7 1.8 - - - +
110A ARG* 4.2 31.5 - - + +
130A ILE* 1.3 76.4 - - - +
132A TRP* 1.3 75.4 + - - +
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Residues in contact with TRP 132 (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 TYR* 3.8 28.5 - + + -
54A HIS 4.1 2.9 - - - -
55A TYR* 3.5 38.5 - + + -
56A GLU* 5.8 0.3 - - - +
103A ALA* 5.2 2.0 - - + -
106A ILE* 5.7 2.9 - - + +
107A GLY 3.8 21.2 + - - +
108A ASN* 3.2 29.5 + - - +
109A GLU 5.0 1.2 + - - -
131A LYS* 1.3 89.2 - - - +
133A LEU* 1.3 74.8 + - - +
134A ALA* 3.4 31.6 - - - -
135A ILE* 3.4 32.5 - - + -
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Residues in contact with LEU 133 (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 HIS* 3.1 45.5 + - + +
56A GLU* 3.8 39.7 - - + +
97A ASN* 5.9 0.2 - - - +
132A TRP* 1.3 91.9 + - - +
134A ALA* 1.3 77.3 + - + +
155A GLU* 6.4 0.4 - - - -
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Residues in contact with ALA 134 (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 HIS* 3.2 31.5 + - + +
132A TRP* 3.4 16.6 - - - -
133A LEU* 1.3 96.7 - - + +
135A ILE* 1.3 66.6 + - - +
136A VAL* 5.8 1.8 - - + -
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ASP* 3.6 38.8 - - + +
52A VAL 3.8 3.4 - - - +
53A TYR* 4.1 21.1 - - + +
132A TRP* 3.4 24.1 - - + -
134A ALA* 1.3 78.4 - - - +
136A VAL* 1.3 67.9 + - - +
137A SER* 4.2 3.4 + - - +
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Residues in contact with VAL 136 (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 ASP* 3.4 1.9 - - - -
52A VAL* 2.7 60.9 + - + +
54A HIS* 4.2 21.5 - - + +
99A TYR* 4.6 4.3 - - + -
134A ALA* 3.9 2.4 + - + -
135A ILE* 1.3 77.7 - - - +
137A SER* 1.3 59.8 + - - +
138A TRP* 4.4 2.2 - - + -
155A GLU* 3.5 48.9 - - + +
156A SER* 3.5 20.2 - - - +
159A ALA* 4.3 2.5 - - + -
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Residues in contact with SER 137 (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 ASP* 3.5 20.3 + - - -
135A ILE* 4.1 4.1 + - - -
136A VAL* 1.3 72.0 - - - +
138A TRP* 1.3 59.2 + - - +
139A ARG* 3.4 9.7 + - - +
140A MET* 2.9 47.3 + - - +
141A LEU 3.5 8.5 + - - -
156A SER* 2.7 25.3 + - - -
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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