Contacts of the strand formed by residues 139 - 149 (chain I) in PDB entry 2B4X
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 LYS 139 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I LYS* 6.4 1.8 - - - +
137I SER* 3.7 0.8 - - - +
138I SER* 1.3 76.6 - - - +
140I LEU* 1.3 61.1 + - - +
141I VAL* 5.2 4.0 - - - -
220I LEU* 3.5 4.9 - - - +
221I PHE* 3.8 3.1 - - - -
222I LYS* 3.2 38.2 + - - +
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Residues in contact with LEU 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81I LEU* 5.3 1.6 - - + -
130I LEU* 3.5 39.0 - - + +
131I TYR* 3.5 31.4 - - + +
138I SER 4.0 3.0 + - - +
139I LYS* 1.3 71.3 - - - +
141I VAL* 1.3 67.3 + - - +
219I ILE* 4.4 14.1 - - + -
220I LEU 3.5 1.3 - - - +
221I PHE* 3.5 42.6 - - + -
279I ILE* 4.7 9.0 - - + -
421I ILE* 3.5 30.3 - - + -
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Residues in contact with VAL 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131I TYR* 4.1 5.2 - - - -
139I LYS* 5.2 1.8 - - - -
140I LEU* 1.3 82.1 - - - +
142I SER* 1.3 71.9 + - - +
143I ALA* 3.9 2.1 + - + +
193I LYS* 4.5 22.7 - - + +
194I THR* 6.4 0.2 - - + -
195I GLU* 5.9 1.6 - - - +
219I ILE* 3.4 7.6 - - - +
220I LEU* 2.9 57.6 + - + +
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Residues in contact with SER 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I THR* 5.1 2.6 - - - +
131I TYR* 3.5 39.6 + - - -
141I VAL* 1.3 80.6 - - - +
143I ALA* 1.3 61.2 + - - +
144I ASN* 3.4 26.5 + - - +
166I TYR 5.1 7.0 + - - -
167I GLY 5.7 0.9 - - - +
189I TRP* 5.3 2.4 - - - -
193I LYS* 5.5 1.4 - - - +
218I THR 4.1 2.7 - - - -
219I ILE* 4.3 2.8 - - - +
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Residues in contact with ALA 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141I VAL* 3.9 3.5 + - + +
142I SER* 1.3 72.7 + - - +
144I ASN* 1.3 61.9 + - - +
189I TRP* 4.2 17.3 - - + -
190I VAL* 4.7 4.7 - - + -
193I LYS* 4.5 14.1 - - + -
194I THR* 4.1 14.6 - - + -
216I VAL* 3.7 3.1 - - - +
217I ASN* 3.5 3.5 - - - -
218I THR* 2.9 56.2 + - + +
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Residues in contact with ASN 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I SER* 3.6 12.8 + - - +
85I THR* 3.7 29.5 - - - +
86I ALA* 3.9 7.2 - - + +
89I MET* 3.5 20.4 - - + +
142I SER* 3.4 22.1 + - - +
143I ALA* 1.3 75.4 - - - +
145I ARG* 1.3 66.2 + - - +
166I TYR 5.3 1.7 - - - +
168I ALA* 3.2 22.2 - - - +
189I TRP* 3.7 3.7 - - - -
215I LEU* 6.2 0.2 - - + -
216I VAL 3.5 2.7 - - - +
217I ASN* 2.8 35.3 - - + +
218I THR 3.1 9.2 + - - +
219I ILE* 5.1 1.4 - - - +
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Residues in contact with ARG 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I MET* 4.4 8.0 - - - +
144I ASN* 1.3 77.7 - - - +
146I LEU* 1.3 71.3 + - - +
147I PHE* 4.2 18.9 - - + -
167I GLY 4.9 0.6 + - - -
168I ALA* 3.6 28.8 - - + +
169I LYS* 3.6 29.8 + - - +
170I LEU 3.9 0.2 - - - +
171I GLN* 4.1 24.4 + - - +
189I TRP* 3.4 48.7 - - + +
215I LEU* 3.4 6.3 - - - +
216I VAL* 3.0 35.6 + - - +
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Residues in contact with LEU 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I MET* 4.7 9.5 - - - -
90I THR* 4.1 23.1 - - + +
145I ARG* 1.3 77.6 - - - +
147I PHE* 1.3 72.8 + - - +
158I TYR* 4.0 26.2 - - + +
169I LYS 4.9 0.8 + - - -
170I LEU* 2.5 35.0 + - - +
171I GLN 3.6 0.2 - - - +
213I LEU* 3.8 36.8 - - + -
214I VAL 3.8 7.4 - - - +
215I LEU* 3.4 29.2 - - + -
351I LEU* 6.1 0.4 - - + -
354I ILE* 5.8 7.4 - - + -
364I VAL* 5.5 1.1 - - + -
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Residues in contact with PHE 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145I ARG* 4.2 24.2 - - + -
146I LEU* 1.3 79.0 - - - +
148I GLY* 1.3 57.6 + - - +
171I GLN* 3.3 36.3 - - + -
173I LEU* 4.2 13.5 - - + -
175I PHE* 4.1 11.4 - - + -
185I ALA 5.5 1.3 - - - -
186I ILE* 3.4 58.1 - - + -
189I TRP* 4.6 11.9 - + + -
212I VAL 3.9 0.2 - - - +
213I LEU* 3.1 7.8 - - - +
214I VAL* 2.6 52.0 + - + +
216I VAL* 4.0 19.7 - - + -
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Residues in contact with GLY 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I LEU 4.3 0.6 - - - -
147I PHE* 1.3 75.1 - - - +
149I ASP* 1.3 59.5 + - - -
171I GLN 3.8 4.9 + - - -
172I PRO* 3.0 7.2 - - - +
173I LEU 2.7 27.5 + - - -
175I PHE* 3.2 6.3 - - - -
212I VAL 3.1 12.3 - - - -
213I LEU* 3.6 12.7 - - - +
362I LEU* 5.9 0.7 - - - -
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Residues in contact with ASP 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148I GLY* 1.3 74.8 - - - +
150I LYS* 1.3 67.8 + - - +
151I SER* 2.7 41.4 + - - +
172I PRO* 3.5 6.2 - - - +
173I LEU 3.1 7.0 - - - -
174I ASP* 4.0 4.7 - - - +
175I PHE* 3.0 51.5 + - + +
176I LYS* 5.0 0.9 - - - +
211I THR 5.2 1.1 - - - +
212I VAL* 3.1 11.1 + - + +
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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