Contacts of the strand formed by residues 162 - 172 (chain B) in PDB entry 3AFF
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 ARG 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A PRO 4.9 0.6 + - - -
123A MET* 3.0 52.2 + - - +
124A GLY* 4.4 8.3 - - - -
125A ALA* 4.6 1.1 - - - -
136A ASN* 4.5 4.0 - - + +
137A GLY* 4.5 6.3 - - - -
138A SER* 3.4 28.5 + - - +
158B ILE* 3.7 5.5 - - - +
159B LYS 2.8 34.1 + - - +
160B ASP 4.3 4.0 - - - +
161B GLY* 1.3 78.3 - - - +
163B PRO* 1.4 89.3 + - + +
164B VAL* 3.4 8.9 - - + +
383B HIS* 5.6 7.5 - - - -
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Residues in contact with PRO 163 (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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122A PRO 5.7 4.3 - - - +
124A GLY* 4.5 10.1 - - - +
125A ALA* 4.5 13.5 - - + -
156A PRO* 5.1 9.2 - - + -
156B PRO* 4.5 7.2 - - + -
157B VAL 3.2 10.5 - - - +
158B ILE* 4.2 14.6 - - + -
162B ARG* 1.4 103.8 + - + +
164B VAL* 1.3 57.6 + - - +
165B ASP 3.8 0.2 - - - -
383B HIS* 4.7 6.2 + - - +
385B PHE* 3.7 44.4 - - + +
386B GLY* 3.9 5.0 + - - +
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 5.0 0.4 - - + -
157B VAL* 2.9 31.4 + - + +
159B LYS* 3.9 41.7 - - + +
162B ARG* 3.4 18.2 - - + +
163B PRO* 1.3 78.2 - - - +
165B ASP* 1.3 69.5 + - + +
383B HIS* 3.3 26.9 + - - -
386B GLY* 4.0 0.4 - - - -
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Residues in contact with ASP 165 (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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133B TYR* 5.5 0.9 + - - -
156B PRO* 3.2 5.4 - - - +
157B VAL* 2.6 45.9 + - + +
164B VAL* 1.3 85.5 - - + +
166B PHE* 1.3 68.5 + - - +
207B PHE* 3.6 19.1 - - - -
209B SER* 2.9 27.2 + - - -
211B LYS* 4.9 5.2 - - - +
383B HIS* 4.7 0.9 - - - -
385B PHE 3.6 4.5 - - - +
386B GLY* 3.4 15.1 - - - +
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Residues in contact with PHE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A PHE* 3.9 24.2 - + - -
120B TYR 4.6 4.7 - - - -
122B PRO* 3.9 7.2 - - + -
154B GLY 4.5 0.7 - - - -
155B GLY* 3.6 32.1 - - - -
156B PRO* 3.5 13.5 - - + -
165B ASP* 1.3 81.5 + - - +
167B GLY* 1.3 76.9 + - - +
207B PHE* 3.6 6.7 - - - -
209B SER* 3.5 4.7 + - - -
210B TYR* 3.0 54.6 + + - +
211B LYS 4.6 0.3 + - - -
377B TYR* 3.6 18.8 - + - -
385B PHE 3.6 13.2 - - - -
386B GLY 3.3 18.6 + - - +
387B LEU* 3.6 24.9 - - + +
388B PRO* 5.1 1.1 - - + +
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Residues in contact with GLY 167 (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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153B VAL 4.0 0.2 - - - +
154B GLY* 3.4 4.9 - - - -
155B GLY 3.1 30.5 + - - +
166B PHE* 1.3 80.9 - - - +
168B SER* 1.3 62.8 + - - -
169B PHE* 4.5 0.5 - - - -
207B PHE* 3.5 11.4 - - - -
208B LEU 3.2 12.3 - - - -
210B TYR* 3.8 16.8 - - - -
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Residues in contact with SER 168 (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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95B HIS* 3.3 31.8 + - - -
99B PHE* 3.7 12.5 - - - -
120B TYR* 3.8 9.3 - - - -
152B PHE* 4.2 14.4 - - - -
153B VAL 3.5 7.2 - - - -
154B GLY* 5.2 0.2 - - - -
167B GLY* 1.3 74.9 + - - -
169B PHE* 1.3 59.1 + - - +
207B PHE* 3.3 7.4 - - - -
208B LEU 2.8 36.5 + - - -
210B TYR* 3.7 13.0 - - - -
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Residues in contact with PHE 169 (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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125B ALA 4.7 1.8 - - - -
126B GLY* 3.7 27.1 - - - -
133B TYR* 3.7 34.3 - + + -
135B VAL* 3.7 22.9 - - + -
139B TRP* 5.5 1.6 - + - -
151B THR 3.5 1.4 - - - +
152B PHE* 3.3 5.5 - - - -
153B VAL* 2.8 59.0 + - + +
154B GLY 4.8 0.4 - - - -
155B GLY* 3.8 25.1 - - - -
156B PRO 4.0 0.9 - - - -
157B VAL* 4.0 10.1 - - + -
167B GLY 4.5 0.7 - - - -
168B SER* 1.3 72.1 - - - +
170B LEU* 1.3 59.0 + - - +
171B ILE* 3.9 5.0 + - + +
202B VAL* 4.2 11.7 - - + -
206B ARG 3.6 2.9 - - - -
207B PHE* 3.4 30.3 - + - -
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Residues in contact with LEU 170 (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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96B LEU* 3.9 15.9 - - + -
99B PHE* 3.9 12.1 - - + -
103B ALA* 3.9 21.1 - - + +
107B VAL* 3.8 23.8 - - + -
116B ILE* 4.0 6.3 - - + -
150B TRP* 3.5 34.5 - - + -
151B THR 3.4 12.6 - - - +
152B PHE* 3.8 19.3 - - + -
168B SER 4.2 0.4 + - - -
169B PHE* 1.3 70.1 - - - +
171B ILE* 1.3 63.0 + - - +
172B PRO* 4.5 0.5 - - - +
202B VAL* 4.0 5.9 - - - +
206B ARG* 2.8 47.1 + - + +
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Residues in contact with ILE 171 (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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135B VAL* 4.1 5.4 - - + -
150B TRP* 3.4 5.1 - - - -
151B THR* 3.0 35.7 + - + +
153B VAL* 4.0 20.4 - - + -
169B PHE* 4.1 9.2 - - + +
170B LEU* 1.3 80.1 - - - +
172B PRO* 1.4 81.5 - - + +
175B GLU* 3.9 16.4 - - + +
176B TYR* 3.4 18.2 - - + -
197B VAL* 3.8 29.6 - - + -
200B VAL* 4.1 7.4 - - + -
202B VAL* 3.8 24.0 - - + -
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Residues in contact with PRO 172 (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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149B SER 3.8 1.3 - - - +
150B TRP* 3.3 42.3 - - + -
170B LEU 4.5 0.2 - - - +
171B ILE* 1.4 85.0 - - + +
173B ARG* 1.3 59.4 + - - +
174B SER* 4.3 10.3 - - - +
175B GLU* 2.9 53.0 + - - +
176B TYR* 3.3 9.2 - - - -
202B VAL* 6.4 0.4 - - + -
206B ARG* 4.4 10.3 - - - +
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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