Contacts of the strand formed by residues 124 - 138 (chain A) in PDB entry 4PH8
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 GLY 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A HIS* 3.8 9.0 - - - -
70A LYS* 6.3 1.1 - - - -
122A ILE 3.7 0.2 + - - -
123A PRO* 1.3 76.8 - - - +
125A GLU* 1.3 66.6 + - - -
126A TYR* 4.1 2.9 - - - -
153A LEU 4.0 0.5 - - - +
154A THR* 3.6 4.4 - - - +
155A VAL* 2.9 36.1 + - - +
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A HIS* 3.6 9.2 + - - -
69A ALA* 3.0 40.7 + - + +
70A LYS* 6.3 0.6 - - - +
124A GLY* 1.3 74.6 - - - -
126A TYR* 1.3 63.6 + - - +
127A THR* 6.0 2.7 - - + -
152A ARG* 6.0 1.7 - - - +
153A LEU 4.0 2.3 - - - +
154A THR* 2.6 39.5 + - - +
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Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.7 39.5 - - + -
67A GLN 3.3 7.0 - - - -
68A HIS* 3.5 42.0 - + + -
74A GLN* 3.4 22.1 + - + -
75A LYS* 5.2 0.4 - - - -
76A TYR* 5.5 5.3 - + - -
120A VAL 5.1 0.3 + - - -
121A LEU* 6.1 2.2 - - + -
122A ILE* 3.2 48.8 + - - +
124A GLY 4.1 2.7 - - - -
125A GLU* 1.3 78.5 - - - +
127A THR* 1.3 65.6 + - - +
152A ARG* 3.5 5.2 - - - +
153A LEU* 2.8 42.6 + - + +
155A VAL* 3.6 22.9 - - + -
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Residues in contact with THR 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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65A VAL 3.4 1.2 - - - +
66A LEU* 4.2 1.8 - - - -
67A GLN* 2.8 41.8 + - - +
69A ALA* 5.9 6.9 - - + +
125A GLU* 5.7 3.6 - - + -
126A TYR* 1.3 79.0 - - - +
128A MET* 1.3 61.1 + - - +
129A ILE* 4.2 4.0 - - - +
150A THR* 3.6 15.0 - - + -
151A ILE 3.2 5.2 - - - -
152A ARG* 3.3 31.4 - - + +
93B THR* 5.2 10.2 - - - +
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Residues in contact with MET 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 3.7 40.2 - - + -
64A TRP* 3.8 29.2 - - + -
65A VAL 3.3 28.3 - - - +
66A LEU* 3.9 15.0 - - + -
78A LEU* 4.2 11.4 - - - -
112A VAL* 3.9 8.3 - - + -
127A THR* 1.3 74.5 - - - +
129A ILE* 1.3 62.7 + - - +
130A LEU* 3.7 9.8 + - + +
149A GLN 3.8 0.2 - - - +
150A THR* 3.4 1.8 - - - -
151A ILE* 2.7 57.6 + - + +
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Residues in contact with ILE 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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57A GLY* 4.0 12.1 - - - -
58A THR* 3.9 17.4 + - + +
65A VAL 4.2 4.7 + - - -
127A THR* 5.3 4.3 - - - +
128A MET* 1.3 75.1 - - - +
130A LEU* 1.3 72.4 + - - +
131A HIS* 4.0 7.9 - - - +
148A THR* 3.4 19.1 - - - +
149A GLN 3.8 4.0 - - - +
150A THR* 4.0 15.0 - - + +
90B ASN 4.2 1.8 - - - +
91B GLN* 3.2 39.0 - - + +
92B GLY* 4.3 3.4 - - - +
93B THR* 3.4 35.9 - - + +
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Residues in contact with LEU 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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18A ILE* 4.5 6.5 - - + +
20A THR* 4.6 2.7 - - + -
38A ALA* 3.6 31.4 - - + -
55A LEU* 4.5 9.2 - - + -
56A TRP 3.7 6.7 - - - +
57A GLY* 4.4 0.4 - - - -
64A TRP* 3.4 53.4 - - + +
128A MET* 4.4 7.2 - - + +
129A ILE* 1.3 85.0 - - - +
131A HIS* 1.3 62.6 + - - +
148A THR* 2.9 18.6 + - - -
149A GLN 2.9 26.7 + - - +
151A ILE* 3.6 26.5 - - + -
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Residues in contact with HIS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 5.1 0.4 - - - -
55A LEU* 3.3 8.1 - - - +
56A TRP* 2.8 81.7 + + + +
57A GLY 4.7 0.2 - - - -
58A THR* 3.8 22.4 - - + +
129A ILE* 4.2 1.1 - - + -
130A LEU* 1.3 78.5 - - - +
132A ALA* 1.3 60.5 + - - +
146A GLN* 4.6 6.6 + - - -
147A THR 3.5 8.8 + - - +
148A THR* 4.2 12.5 + - - -
88B PHE* 4.7 13.0 - + + -
91B GLN* 2.9 35.5 + - - +
92B GLY 4.7 0.4 - - - -
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Residues in contact with ALA 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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16A VAL* 3.8 17.2 - - + +
18A ILE* 3.9 18.2 - - + -
40A VAL* 3.8 19.1 - - + -
54A TRP 3.2 12.6 - - - +
56A TRP* 3.9 2.9 - - - -
130A LEU 4.3 0.2 + - - -
131A HIS* 1.3 75.5 - - - +
133A ALA* 1.3 63.2 + - - +
146A GLN* 3.1 5.4 - - - +
147A THR* 2.9 36.2 + - + +
148A THR* 4.9 0.2 - - - +
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Residues in contact with ALA 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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16A VAL* 3.8 8.7 - - - +
40A VAL* 4.4 0.2 - - - +
53A VAL* 3.2 7.6 - - - +
54A TRP* 2.8 42.0 + - + +
56A TRP* 3.7 22.3 - - + -
132A ALA* 1.3 77.2 - - - +
134A VAL* 1.3 62.3 - - - +
135A ASP* 5.1 3.4 - - - +
144A SER* 5.1 4.0 - - - +
145A GLN 3.1 14.4 - - - +
146A GLN* 3.8 6.1 - - + -
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A CYS* 3.6 33.0 - - + +
15A PRO 3.5 23.6 - - - +
16A VAL* 3.9 4.7 - - + -
42A THR* 4.1 6.1 - - - -
51A ALA* 3.8 28.0 - - + -
52A LYS 3.3 6.3 - - - +
53A VAL* 4.0 13.9 - - + +
133A ALA* 1.3 74.5 - - - +
135A ASP* 1.3 66.3 + - - +
136A PHE* 3.5 2.5 - - + -
144A SER* 3.1 5.5 - - - -
145A GLN* 2.9 35.3 + - + +
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Residues in contact with ASP 135 (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 GLY 4.8 0.3 - - - +
51A ALA* 3.4 6.6 - - - +
52A LYS* 2.8 41.7 + - + +
54A TRP* 2.7 37.2 + - - +
133A ALA* 5.1 1.4 - - - +
134A VAL* 1.3 73.3 - - - +
136A PHE* 1.3 65.8 + - - +
143A ALA 3.5 5.8 - - - +
144A SER* 3.2 21.4 - - - -
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Residues in contact with PHE 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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10A VAL* 3.7 20.4 - - + -
13A ASP* 3.4 39.7 - - + -
14A CYS* 3.4 44.2 - - + -
46A CYS 5.9 0.2 - - - +
49A ALA* 6.1 2.9 - - + -
50A GLY 6.0 0.7 - - - -
51A ALA* 4.8 7.4 - - + +
134A VAL* 3.5 17.7 - - + -
135A ASP* 1.3 79.8 - - - +
137A ASP* 1.3 72.1 + - - +
138A ASN* 4.1 2.7 - - - -
142A GLY* 3.7 0.7 - - - -
143A ALA* 2.9 44.7 + - + +
144A SER* 3.9 11.2 - - - -
145A GLN* 3.9 12.6 - - + -
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Residues in contact with ASP 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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8A HIS 3.8 20.7 + - - +
9A HIS* 3.2 10.0 - - + -
10A VAL* 2.9 29.1 + - - +
136A PHE* 1.3 83.3 - - - +
138A ASN* 1.3 63.1 + - - +
141A GLY* 3.3 11.5 - - - +
142A GLY* 3.6 12.3 - - - -
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Residues in contact with ASN 138 (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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9A HIS* 3.9 11.2 - - - +
10A VAL* 3.3 18.2 - - + +
11A THR* 5.4 2.0 - - - -
13A ASP* 3.0 29.3 + - - +
136A PHE* 4.2 6.0 - - + -
137A ASP* 1.3 75.0 - - - +
139A LYS* 1.3 66.1 + - - +
140A GLN* 3.0 29.8 + - - +
141A GLY* 2.9 28.3 + - - +
143A ALA* 3.7 18.7 - - - +
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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