Contacts of the strand formed by residues 142 - 151 (chain G) in PDB entry 4BEI
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 VAL 142 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135G VAL 3.5 7.4 - - - +
136G VAL* 4.4 6.5 - - + -
140G GLY 3.7 13.0 - - - +
141G LYS* 1.3 74.3 - - - +
143G PHE* 1.3 68.1 + - - +
144G LYS* 4.1 13.1 - - + +
210H ASP* 3.7 40.4 - - + +
212H LEU* 3.6 31.4 - - + -
243H PRO* 4.2 15.3 - - + -
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Residues in contact with PHE 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G VAL* 3.9 17.5 - - + -
40G ILE* 3.2 64.6 - - + +
42G ALA* 4.7 8.1 - - + +
134G GLN* 3.6 0.2 - - - -
135G VAL* 2.8 49.2 + - + +
137G ALA* 4.1 5.8 - - + -
141G LYS* 3.5 40.2 - - + -
142G VAL* 1.3 79.1 - - - +
144G LYS* 1.3 66.2 + - - +
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Residues in contact with LYS 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G ALA* 4.4 10.6 - - - +
132G SER* 4.3 2.5 - - - +
133G LEU 3.2 12.1 - - - +
134G GLN* 4.1 27.1 - - + +
142G VAL* 4.1 12.3 - - + +
143G PHE* 1.3 81.1 - - - +
145G ALA* 1.3 62.6 + - - +
146G ASN* 4.2 14.4 - - - +
246G GLU* 2.7 37.4 + - - -
210H ASP 2.8 25.9 + - - +
211H GLY* 3.7 3.3 + - - +
212H LEU* 5.0 0.2 - - + -
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Residues in contact with ALA 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G ALA* 3.5 26.9 - - + +
43G ASN* 3.7 18.2 - - - -
44G LEU* 3.3 17.6 - - + +
133G LEU* 2.8 38.5 + - + +
144G LYS* 1.3 74.1 - - - +
146G ASN* 1.3 61.5 + - - +
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Residues in contact with ASN 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G LEU* 4.4 0.2 - - - -
130G THR* 3.8 19.5 - - + +
131G VAL 3.2 8.5 - - - +
132G SER* 3.1 30.3 + - - -
144G LYS* 4.2 13.7 - - - +
145G ALA* 1.3 84.2 + - - +
147G GLN* 1.3 76.4 + - - +
148G GLU* 6.3 0.7 - - + -
1272G O4B 5.0 8.7 - - - +
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Residues in contact with GLN 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G LEU* 3.0 38.3 - - + +
45G SER* 4.1 5.4 - - - -
46G LEU* 3.6 34.5 - - + +
49G ASN* 5.4 4.9 - - - +
130G THR* 3.6 3.1 - - - +
131G VAL* 2.7 39.5 + - - +
146G ASN* 1.3 81.6 + - - +
148G GLU* 1.3 66.2 + - - +
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Residues in contact with GLU 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G LEU* 3.6 4.7 - - - +
49G ASN* 3.6 20.3 + - - +
128G LYS* 4.7 17.3 - - + +
129G TYR 3.3 10.5 - - - +
130G THR* 4.6 14.9 + - + +
146G ASN* 6.0 0.7 - - + -
147G GLN* 1.3 82.3 + - - +
149G PHE* 1.3 68.2 + - - +
150G VAL* 6.4 0.2 - - + -
155G LEU* 4.9 11.0 - - + +
156G ASN* 4.4 15.1 + - - -
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Residues in contact with PHE 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G LEU* 4.2 6.7 - - + -
49G ASN* 3.2 24.0 - - - +
51G LEU* 4.0 13.0 - - + -
58G ILE* 3.7 22.2 - - + -
80G ILE* 4.2 8.1 - - + -
118G PHE* 4.2 5.4 - + - -
120G VAL* 3.9 21.5 - - + -
128G LYS* 3.9 1.6 - - - +
129G TYR* 2.8 76.7 + + + +
131G VAL* 3.3 35.4 - - + -
148G GLU* 1.3 76.5 - - - +
150G VAL* 1.3 78.8 + - - +
151G LYS* 5.0 0.7 - - + -
155G LEU* 5.4 2.2 - - - -
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Residues in contact with VAL 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G ASN 2.8 16.6 + - - +
50G GLN* 4.0 10.1 - - + -
51G LEU* 2.9 28.5 + - - +
127G GLY 3.4 7.0 - - - +
128G LYS* 4.3 15.7 - - + -
149G PHE* 1.3 85.5 - - - +
151G LYS* 1.3 61.4 + - - +
153G VAL* 3.1 35.2 - - + +
154G ASP 4.0 12.3 - - - +
155G LEU* 3.6 30.7 - - + +
156G ASN 4.7 2.0 - - - +
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Residues in contact with LYS 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G LEU* 3.3 10.8 - - + -
52G ALA 3.7 9.2 - - - +
53G SER 2.9 26.6 + - - -
55G GLY* 3.7 13.0 - - - -
120G VAL* 3.9 19.3 - - + -
121G PRO 3.4 21.5 - - - -
122G GLU 3.1 7.1 + - - -
124G MET 2.7 23.1 + - - +
125G ALA 3.9 9.6 - - - +
126G ASP* 3.1 20.2 + - - +
127G GLY 2.8 34.2 + - - +
129G TYR* 4.0 18.4 - - + +
149G PHE* 5.0 0.9 - - + -
150G VAL* 1.3 75.6 - - - +
152G GLY* 1.3 61.1 + - - +
153G VAL 3.2 4.3 + - - -
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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