Contacts of the strand formed by residues 141 - 148 (chain B) in PDB entry 1P4D
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 MET 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B TRP* 3.3 14.0 - - - -
34B ALA* 2.8 43.7 + - + +
35B GLY* 3.7 29.8 - - - +
55B LEU* 6.0 0.2 - - - -
82B LEU* 6.2 0.2 - - - -
114B VAL* 3.1 46.7 - - + +
117B VAL* 5.7 2.5 - - - -
118B GLU* 4.9 3.4 - - - -
139B LEU* 4.2 24.0 - - + -
140B VAL* 1.3 80.4 - - - +
142B ALA* 1.3 61.3 + - - +
143B LEU* 4.1 9.6 - - + -
160B ALA* 5.2 0.4 - - - -
161B VAL 3.1 5.4 - - - +
162B VAL* 3.7 31.0 - - + -
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Residues in contact with ALA 142 (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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32B ARG 3.7 4.3 - - - -
33B TRP* 4.0 11.7 - - + -
47B VAL* 4.5 5.2 - - + -
52B PHE* 3.4 38.1 - - + -
55B LEU* 6.0 0.2 - - - +
141B MET* 1.3 75.6 - - - +
143B LEU* 1.3 60.1 + - - +
144B PHE* 3.4 15.5 - - + -
159B HIS 3.3 2.6 - - - +
161B VAL* 2.8 34.9 + - - +
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Residues in contact with LEU 143 (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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31B GLU* 2.9 30.5 - - - +
32B ARG* 2.9 56.1 + - - +
34B ALA* 4.4 17.3 - - + -
47B VAL* 5.3 0.2 - - - +
110B VAL* 3.8 19.3 - - + -
111B ASP* 4.1 5.4 - - - +
114B VAL* 4.6 9.9 - - + -
141B MET* 4.4 11.2 - - + -
142B ALA* 1.3 75.6 - - - +
144B PHE* 1.3 61.3 + - - +
158B THR* 4.0 8.1 - - + -
159B HIS 3.4 2.0 - - - -
160B ALA* 3.2 37.9 - - + -
161B VAL 4.3 0.2 - - - +
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Residues in contact with PHE 144 (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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17B TYR* 3.8 33.9 - + + +
18B THR* 3.8 18.4 - - + -
29B MET* 3.9 16.2 - - + -
31B GLU* 3.7 23.3 - - + -
47B VAL* 4.4 11.9 - - + -
52B PHE* 3.7 22.0 - + - -
142B ALA* 3.4 35.7 - - + -
143B LEU* 1.3 73.0 - - - +
145B ASN* 1.3 65.0 + - - +
146B HIS* 3.7 10.6 + - - +
158B THR* 3.3 2.6 - - - +
159B HIS* 2.9 42.3 + - + +
161B VAL* 3.5 17.3 - - + -
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Residues in contact with ASN 145 (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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23B TYR* 3.5 18.5 - - - +
26B LEU* 4.0 15.9 - - + +
28B SER 4.9 0.2 - - - +
29B MET* 3.1 27.4 + - - +
30B GLY* 4.6 6.7 - - - +
32B ARG* 3.8 8.9 + - - +
103B ILE* 4.6 8.5 - - - +
106B HIS* 4.7 3.5 + - - -
107B ASN* 2.9 32.3 + - - +
143B LEU 4.4 0.2 - - - -
144B PHE* 1.3 71.4 - - - +
146B HIS* 1.3 66.8 + - - +
156B LEU* 5.2 2.8 - - + +
157B HIS 3.5 4.5 - - - +
158B THR* 2.5 36.9 + - - +
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Residues in contact with HIS 146 (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 TYR* 4.2 5.4 - + - -
17B TYR* 2.9 38.6 + + - -
22B ASN* 3.2 43.7 - - + +
23B TYR* 4.8 3.1 - + - -
26B LEU* 3.9 7.4 - - - +
144B PHE* 3.7 10.1 + - + +
145B ASN* 1.3 82.6 - - - +
147B ASP* 1.3 61.1 + - - +
148B THR 4.7 0.7 - - - +
156B LEU* 3.9 3.1 - - - +
157B HIS* 2.9 50.0 + - + +
159B HIS* 3.2 20.5 - + - -
901B MG 2.3 27.2 - - - -
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Residues in contact with ASP 147 (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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21B ASP 4.7 0.2 - - - +
22B ASN 3.1 14.0 + - - +
23B TYR* 3.2 14.2 - - - -
24B TYR 4.4 0.7 + - - -
25B VAL* 3.0 36.4 + - - -
26B LEU* 3.3 17.6 + - + -
95B MET* 3.6 23.9 - - - +
146B HIS* 1.3 73.0 - - - +
148B THR* 1.3 87.9 + - - +
154B PRO* 3.7 3.6 - - - +
155B GLN 2.9 30.8 + - - -
156B LEU* 4.6 0.9 - - - +
273B LYS* 4.0 5.9 + - - -
277B TRP* 4.1 1.0 - - - -
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Residues in contact with THR 148 (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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21B ASP 5.9 0.7 - - - -
22B ASN* 4.6 3.3 + - - -
146B HIS* 3.9 1.7 - - - +
147B ASP* 1.3 99.9 + - - +
149B SER* 1.3 76.8 + - - +
152B GLN* 3.9 22.2 - - + -
153B GLU 3.6 5.2 - - - +
155B GLN* 3.6 1.2 + - - -
157B HIS* 3.5 17.4 - - - -
273B LYS* 2.7 33.8 + - + +
277B TRP* 3.6 3.3 - - - -
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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