Contacts of the strand formed by residues 131 - 140 (chain I) in PDB entry 4R2G
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 ALA 131 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121I PRO* 4.0 6.7 - - + -
125I GLU* 3.3 4.3 - - - -
126I LEU* 3.3 28.9 - - + -
130I LYS* 1.3 72.5 - - - +
132I THR* 1.3 65.2 + - - +
180I SER* 3.5 0.9 + - - -
181I LEU* 2.7 61.9 + - + +
183I PRO* 3.9 12.0 - - + +
186I TRP* 4.4 1.3 - - + -
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Residues in contact with THR 132 (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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120I PRO 4.7 0.9 - - - +
121I PRO* 3.9 17.0 - - - +
125I GLU* 2.6 33.2 + - - +
130I LYS* 5.6 0.7 - - + -
131I ALA* 1.3 76.3 - - - +
133I LEU* 1.3 67.9 + - - +
134I VAL* 4.1 6.7 + - - +
178I TYR* 5.8 6.1 - - - -
179I LEU 3.3 8.7 - - - -
180I SER* 3.2 27.8 - - - +
159J LEU* 3.6 16.8 - - - +
161J LYS* 3.7 17.0 - - + +
189J GLN* 6.1 1.6 - - - +
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Residues in contact with LEU 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I LEU* 4.4 1.3 - - + -
119I PHE 3.8 9.4 - - - +
121I PRO* 3.7 32.1 - - + -
132I THR* 1.3 76.0 - - - +
134I VAL* 1.3 65.0 + - - +
135I CYS 4.2 0.4 - - - -
149I TRP* 4.1 14.1 - - + -
178I TYR* 3.4 7.8 - - - +
179I LEU* 2.5 63.8 + - + +
181I LEU* 4.3 17.7 - - + -
186I TRP* 4.0 14.1 - - + -
192I TYR* 3.7 28.5 - - + +
207I VAL* 4.3 7.0 - - + -
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Residues in contact with VAL 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I THR 3.5 2.4 - - - +
118I LEU* 3.2 4.6 - - - -
119I PHE* 2.8 44.5 + - + +
132I THR* 4.3 8.3 - - - +
133I LEU* 1.3 80.3 - - - +
135I CYS* 1.3 61.0 + - - +
136I LEU* 3.7 31.9 - - + -
177I SER 3.9 2.5 - - - +
178I TYR* 3.8 20.4 - - + -
142J LEU* 4.5 16.6 - - + -
159J LEU* 4.0 19.7 - - + -
197J SER* 3.8 12.1 - - - +
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Residues in contact with CYS 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I VAL* 3.5 28.7 - - - -
117I THR 4.0 1.6 - - - -
118I LEU* 4.1 3.6 - - - +
134I VAL* 1.3 72.5 - - - +
136I LEU* 1.3 60.1 + - - +
137I ILE* 4.0 7.4 + - - +
149I TRP* 3.5 15.4 - - + -
175I ALA 4.1 0.2 - - - +
176I SER* 3.5 3.8 - - - -
177I SER* 2.9 40.1 + - - +
194I CYS* 2.0 44.4 - - + -
196I VAL* 4.0 9.0 - - - -
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Residues in contact with LEU 136 (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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115I SER 3.3 3.8 - - - +
116I VAL* 3.3 4.6 - - - -
117I THR* 2.9 47.3 + - - +
119I PHE* 5.3 2.7 - - + -
134I VAL* 3.7 21.1 - - + -
135I CYS* 1.3 81.0 - - - +
137I ILE* 1.3 60.7 + - - +
138I SER* 4.7 0.2 + - - -
176I SER* 3.7 26.5 - - - +
178I TYR* 4.7 0.2 - - - +
142J LEU* 5.5 0.4 - - + -
184J PHE* 3.6 34.1 - - + -
197J SER* 4.1 18.8 - - - +
199J VAL* 3.5 32.8 - - + -
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Residues in contact with ILE 137 (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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114I PRO* 3.5 27.6 - - + -
115I SER 3.8 1.8 - - - -
116I VAL* 3.8 15.9 - - + -
135I CYS* 4.4 10.3 - - - +
136I LEU* 1.3 75.9 - - - +
138I SER* 1.3 65.2 + - - +
140I PHE* 3.7 17.0 - - + -
145I VAL* 3.9 12.3 - - + -
147I VAL* 3.5 32.5 - - + -
174I ALA* 3.4 2.9 - - - -
175I ALA* 2.7 52.6 + - + +
177I SER* 5.2 3.4 - - - -
196I VAL* 4.0 11.0 - - + -
184J PHE* 3.3 8.5 - - - -
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Residues in contact with SER 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I PRO* 3.2 4.9 - - - +
115I SER* 2.8 46.1 + - - +
136I LEU 4.7 0.3 + - - -
137I ILE* 1.3 73.6 + - - +
139I ASP* 1.3 79.2 + - - +
140I PHE* 3.4 4.9 + - - -
173I TYR 4.1 3.4 - - - -
174I ALA* 4.7 1.8 - - - +
182J HIS* 3.8 10.8 + - - -
184J PHE* 2.9 30.0 - - - -
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Residues in contact with ASP 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I ALA* 3.4 10.9 - - - +
113I ALA 3.0 16.5 - - - +
115I SER* 4.7 11.5 + - - +
138I SER* 1.3 80.5 - - - +
140I PHE* 1.3 57.0 + - - +
170I ASN* 3.0 33.7 + - - +
172I LYS* 3.5 24.2 - - + +
173I TYR 3.3 7.4 + - - -
174I ALA* 5.3 0.4 - - - +
182J HIS* 5.5 1.2 + - - -
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Residues in contact with PHE 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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112I ALA* 3.3 15.7 - - - +
114I PRO* 3.8 14.4 - - + -
137I ILE* 3.7 20.6 - - + -
138I SER 3.7 10.8 - - - -
139I ASP* 1.3 76.6 - - - +
141I TYR* 1.3 60.8 + - - +
142I PRO 3.5 8.3 - - - -
143I GLY* 3.9 18.6 - - - -
144I ALA 4.0 1.8 - - - -
145I VAL* 3.5 35.0 - - + -
165I PRO* 4.3 3.8 - - + -
172I LYS* 3.4 6.9 - - - +
173I TYR* 2.6 56.7 + - + -
174I ALA* 3.4 19.1 - - - -
175I ALA 3.7 6.7 - - - -
198I HIS* 3.4 24.0 - + + +
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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