Contacts of the strand formed by residues 124 - 138 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B HIS* 4.0 6.1 - - - -
123B PRO* 1.3 75.1 - - - +
125B GLU* 1.3 69.5 + - - -
126B TYR* 3.9 2.3 - - - -
153B LEU 3.8 0.7 - - - +
154B THR* 3.5 3.2 - - - -
155B VAL* 2.7 40.1 + - - +
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B HIS* 3.4 8.5 + - - -
69B ALA* 2.7 47.9 + - + +
70B LYS* 6.2 2.0 - - - +
124B GLY* 1.3 74.2 - - - -
126B TYR* 1.3 59.6 + - - +
127B THR* 5.6 3.8 - - + -
152B ARG* 5.7 3.3 - - - +
153B LEU 3.7 2.6 - - - +
154B THR* 2.6 41.9 + - - +
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Residues in contact with TYR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 3.8 31.0 - - + -
67B GLN 3.1 7.0 - - - +
68B HIS* 3.4 38.4 - + + -
69B ALA 4.5 0.2 - - - +
74B GLN* 4.0 10.7 + - + +
76B TYR* 4.2 18.8 - + - -
121B LEU* 3.6 12.6 - - + +
122B ILE* 2.9 49.4 + - - +
124B GLY 3.9 4.7 - - - -
125B GLU* 1.3 77.2 - - - +
127B THR* 1.3 70.8 + - - +
152B ARG* 3.5 2.8 - - - +
153B LEU* 2.7 49.8 + - + +
155B VAL* 3.6 18.6 - - + -
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Residues in contact with THR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL 3.4 1.6 - - - +
66B LEU* 4.2 2.9 - - - -
67B GLN* 2.8 40.7 + - - +
69B ALA* 5.7 6.4 - - + -
125B GLU* 5.4 6.1 - - + -
126B TYR* 1.3 82.1 - - - +
128B MET* 1.3 62.0 + - - +
129B ILE* 4.3 7.5 - - - +
150B THR* 3.6 13.9 - - + -
151B ILE 3.2 4.9 - - - -
152B ARG* 3.5 30.5 - - + +
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Residues in contact with MET 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PHE* 3.6 40.2 - - + -
64B TRP* 3.7 24.7 - - + -
65B VAL 3.1 31.2 - - - +
66B LEU* 4.0 13.7 - - + -
78B LEU* 4.1 12.3 - - - -
112B VAL* 3.7 10.3 - - + -
127B THR* 1.3 74.2 - - - +
129B ILE* 1.3 61.8 + - - +
130B LEU* 3.8 13.7 + - + +
149B GLN 3.8 0.3 - - - +
150B THR* 3.4 3.0 - - - -
151B ILE* 2.8 58.2 + - + +
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLY* 4.0 5.9 - - - -
58B THR* 3.7 38.8 + - + +
65B VAL 4.2 4.0 + - - -
127B THR* 5.2 6.7 - - - +
128B MET* 1.3 75.3 - - - +
130B LEU* 1.3 74.9 + - - +
131B HIS* 4.2 13.5 - - - +
148B THR* 4.6 9.6 - - + +
149B GLN 3.8 3.6 - - - +
150B THR* 3.0 32.3 - - + +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 4.7 6.8 - - + +
20B THR* 4.6 2.9 - - + -
38B ALA* 3.5 31.9 - - + -
55B LEU* 4.5 9.9 - - + -
56B TRP 3.6 6.1 - - - +
57B GLY* 4.3 0.4 - - - -
64B TRP* 3.4 54.5 - - + +
128B MET* 4.3 7.2 - - + +
129B ILE* 1.3 84.5 - - - +
131B HIS* 1.3 63.0 + - - +
148B THR* 3.1 6.9 - - - -
149B GLN 2.9 37.3 + - - +
151B ILE* 3.7 25.8 - - + -
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Residues in contact with HIS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.3 9.2 - - - +
56B TRP* 2.8 80.4 + + + +
57B GLY 4.7 0.4 - - - -
58B THR* 4.0 27.5 - - + +
129B ILE* 4.2 4.8 - - + +
130B LEU* 1.3 77.9 - - - +
132B ALA* 1.3 60.0 + - - +
146B GLN* 4.6 6.8 + - - -
147B THR 3.4 6.2 + - - +
148B THR* 3.2 26.2 - - + +
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL* 3.7 18.1 - - + +
18B ILE* 3.9 27.1 - - + -
40B VAL* 4.0 10.1 - - + -
54B TRP 3.1 13.5 - - - +
55B LEU* 4.2 0.2 - - + -
56B TRP* 3.8 4.2 - - - -
130B LEU 4.3 0.2 + - - -
131B HIS* 1.3 74.8 - - - +
133B ALA* 1.3 60.9 + - - +
146B GLN* 3.1 4.7 - - - +
147B THR* 2.9 34.8 + - + +
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL* 3.9 8.1 - - - +
53B VAL* 3.2 7.8 - - - +
54B TRP* 2.8 38.5 + - + +
56B TRP* 3.8 17.4 - - + -
132B ALA* 1.3 77.5 - - - +
134B VAL* 1.3 63.9 + - - +
135B ASP* 4.9 0.4 - - - +
144B SER* 5.3 1.6 - - - -
145B GLN 3.1 13.7 - - - +
146B GLN* 3.9 8.3 - - + -
201B GOL 4.1 15.3 - - - +
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B CYS* 3.4 41.5 - - + +
15B PRO 3.5 15.9 - - - +
16B VAL* 4.0 4.0 - - + -
42B THR* 4.0 7.6 - - - +
51B ALA* 3.8 24.0 - - + -
52B LYS 3.3 9.0 - - - +
53B VAL* 4.0 13.7 - - + -
133B ALA* 1.3 75.4 - - - +
135B ASP* 1.3 66.1 + - - +
136B PHE* 3.8 2.1 - - + -
144B SER* 3.0 6.8 - - - -
145B GLN* 2.8 40.1 + - + +
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Residues in contact with ASP 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLY 4.8 0.2 - - - +
51B ALA* 3.4 6.4 - - - +
52B LYS* 2.8 40.3 + - + +
54B TRP* 2.8 33.2 + - - +
134B VAL* 1.3 73.4 - - - +
136B PHE* 1.3 64.1 + - - +
143B ALA 3.4 5.8 - - - +
144B SER* 3.1 21.9 - - - -
201B GOL 3.2 17.6 + - - -
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Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 3.7 20.0 - - + -
13B ASP* 3.3 35.2 - - + -
14B CYS* 3.4 53.4 - - + -
49B ALA* 6.2 2.5 - - + -
50B GLY 6.1 0.2 - - - -
51B ALA* 4.6 7.0 - - + +
134B VAL 3.8 8.7 - - - -
135B ASP* 1.3 79.9 - - - +
137B ASP* 1.3 72.6 + - - +
138B ASN* 4.1 3.1 - - - -
142B GLY* 3.6 3.5 - - - -
143B ALA* 2.8 46.3 + - + +
144B SER* 3.8 20.2 - - - -
145B GLN* 4.0 9.2 - - + -
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Residues in contact with ASP 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B HIS 3.8 21.0 + - - +
9B HIS* 3.2 8.9 - - + -
10B VAL* 2.9 30.0 + - - +
49B ALA* 6.0 0.2 - - - +
136B PHE* 1.3 82.3 - - - +
138B ASN* 1.3 62.2 + - - +
141B GLY* 3.4 10.9 - - - +
142B GLY* 3.7 17.6 + - - -
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Residues in contact with ASN 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B HIS* 3.9 11.0 - - - +
10B VAL 3.4 17.9 - - - +
11B THR* 5.3 3.4 - - - +
13B ASP* 3.2 29.7 + - - +
136B PHE* 4.2 4.7 - - + -
137B ASP* 1.3 75.8 - - - +
139B LYS* 1.3 65.4 + - - +
140B GLN* 3.0 21.1 + - - +
141B GLY* 3.0 25.9 + - - +
142B GLY 5.0 0.2 - - - +
143B ALA* 3.6 18.9 - - - +
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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