Contacts of the strand formed by residues 142 - 151 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210G ASP* 3.9 39.9 - - + +
212G LEU* 3.7 38.1 - - + -
243G PRO* 4.5 5.4 - - + -
135H VAL 3.5 6.5 - - - +
136H VAL* 4.4 8.3 - - + -
140H GLY 3.5 13.7 + - - +
141H LYS* 1.3 74.8 - - - +
143H PHE* 1.3 69.0 + - - +
144H LYS* 4.1 13.8 - - + +
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Residues in contact with PHE 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H PRO 4.0 9.9 - - - -
39H VAL* 4.2 7.6 - - + -
40H ILE* 3.2 66.2 - - + +
42H ALA* 4.6 8.1 - - + +
135H VAL* 2.8 47.9 + - + +
137H ALA* 4.1 6.5 - - + -
141H LYS* 3.5 41.3 - - + -
142H VAL* 1.3 77.4 - - - +
144H LYS* 1.3 66.9 + - - +
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Residues in contact with LYS 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210G ASP* 2.9 24.3 + - - +
211G GLY* 3.7 3.7 - - - +
42H ALA* 4.4 10.0 - - - +
132H SER* 4.4 2.2 - - - +
133H LEU 3.2 11.9 - - - +
134H GLN* 4.0 26.9 - - + +
142H VAL* 4.1 12.1 - - + +
143H PHE* 1.3 82.6 - - - +
145H ALA* 1.3 61.8 + - - +
146H ASN* 4.2 13.0 - - - +
246H GLU* 2.8 36.8 + - - -
1272H O4B 5.9 0.4 - - - -
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Residues in contact with ALA 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H ALA* 3.5 26.2 - - + +
43H ASN* 3.7 23.8 - - - -
44H LEU* 3.3 13.4 - - + +
133H LEU* 2.8 37.5 + - + -
144H LYS* 1.3 74.1 - - - +
146H ASN* 1.3 61.6 + - - +
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Residues in contact with ASN 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130H THR* 3.8 19.0 - - + +
131H VAL 3.2 8.1 - - - +
132H SER* 3.0 30.1 + - - -
144H LYS* 4.2 14.1 - - - +
145H ALA* 1.3 85.1 + - - +
147H GLN* 1.3 78.3 + - - +
148H GLU* 6.3 0.7 - - + -
1272H O4B 5.1 7.4 - - - +
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Residues in contact with GLN 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H LEU* 3.0 39.6 - - + +
45H SER* 4.1 4.7 - - - -
46H LEU* 3.6 33.6 - - + +
49H ASN* 5.4 4.9 - - - +
130H THR* 3.6 2.9 - - - +
131H VAL* 2.7 39.5 + - - +
146H ASN* 1.3 84.2 + - - +
148H GLU* 1.3 67.3 + - - +
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Residues in contact with GLU 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H LEU* 3.6 5.2 - - - +
49H ASN* 3.6 20.1 + - - +
128H LYS* 6.2 5.2 - - + -
129H TYR 3.3 11.2 - - - +
130H THR* 4.6 14.6 + - + +
146H ASN* 6.0 1.1 - - + -
147H GLN* 1.3 82.7 + - - +
149H PHE* 1.3 67.4 - - - +
150H VAL* 6.4 0.2 - - + -
155H LEU* 5.2 14.9 - - + +
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Residues in contact with PHE 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H LEU* 4.1 7.6 - - + -
49H ASN* 3.2 23.8 - - - +
51H LEU* 4.0 12.3 - - + -
58H ILE* 3.7 23.1 - - + -
80H ILE* 4.2 9.0 - - + -
118H PHE* 4.2 4.9 - + - -
120H VAL* 3.8 22.4 - - + -
128H LYS* 3.9 0.5 - - - +
129H TYR* 2.8 75.4 + + + +
131H VAL* 3.3 34.3 - - + -
148H GLU* 1.3 77.2 - - - +
150H VAL* 1.3 78.9 + - - +
151H LYS* 5.0 0.7 - - + -
155H LEU* 5.2 2.5 - - - -
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Residues in contact with VAL 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49H ASN 2.8 17.4 + - - +
50H GLN* 3.9 9.6 - - - +
51H LEU* 2.9 29.3 + - - +
127H GLY 3.4 7.0 - - - +
128H LYS* 4.3 11.9 - - + -
148H GLU* 6.4 0.2 - - + -
149H PHE* 1.3 84.7 - - - +
151H LYS* 1.3 60.5 + - - +
153H VAL* 3.1 35.0 - - + +
154H ASP 4.0 12.1 - - - +
155H LEU* 3.7 32.1 - - + +
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Residues in contact with LYS 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H LEU* 3.3 11.2 - - + -
52H ALA 3.7 8.3 - - - +
53H SER 2.9 26.8 + - - -
55H GLY* 3.7 13.5 - - - -
120H VAL* 3.9 19.3 - - + -
121H PRO 3.4 21.8 - - - -
122H GLU 3.1 6.7 + - - -
124H MET* 2.7 23.1 + - + +
125H ALA 3.9 10.3 - - - +
126H ASP* 3.1 20.2 + - - +
127H GLY 2.8 35.1 + - - +
129H TYR* 4.0 17.7 - - + +
149H PHE* 5.0 0.9 - - + -
150H VAL* 1.3 75.5 - - - +
152H GLY* 1.3 61.1 + - - +
153H 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