Contacts of the strand formed by residues 135 - 143 (chain A) in PDB entry 3QFR
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 LEU 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A MET* 5.0 0.6 - - - +
82A ASN 3.0 10.7 + - - +
83A ILE* 3.3 31.7 - - + +
84A ILE* 3.0 26.2 + - - +
110A MET* 5.4 0.7 - - - -
128A LEU* 5.2 2.2 - - - +
133A ASN 4.5 1.3 - - - +
134A ALA* 1.3 74.7 - - - +
136A VAL* 1.3 64.5 + - - +
137A VAL* 4.1 11.9 - - + -
170A LYS* 3.7 24.0 - - + +
171A PHE* 4.4 5.2 - - - +
203A ILE* 4.5 13.5 - - + -
226A PHE* 4.0 14.4 - - + -
230A VAL* 3.6 26.2 - - + -
234A PHE* 4.1 22.2 - - + -
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Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ILE* 3.3 13.0 - - + +
86A PHE* 3.8 20.2 - - + -
125A LEU* 4.2 8.1 - - + -
128A LEU* 3.7 27.3 - - + +
135A LEU* 1.3 74.3 - - - +
137A VAL* 1.3 64.0 + - - +
138A PHE* 3.5 29.3 - - + -
169A VAL* 3.8 11.2 - - + -
170A LYS 3.0 16.3 + - - +
171A PHE* 3.1 36.2 - - + +
172A ALA 3.2 3.8 + - - +
195A LEU* 5.9 0.2 - - + -
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ILE* 5.0 3.8 - - + -
84A ILE 2.8 8.7 + - - +
85A VAL* 2.9 25.3 - - + +
86A PHE 2.8 31.5 + - - -
101A LEU* 3.6 27.6 - - + -
135A LEU* 4.1 12.6 - - + -
136A VAL* 1.3 79.6 - - - +
138A PHE* 1.3 64.2 + - - +
139A CYS* 4.8 0.9 - - - -
172A ALA* 3.3 11.7 - - + +
222A TRP* 4.4 13.9 - - + -
226A PHE* 3.4 31.9 - - + -
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Residues in contact with PHE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PHE* 3.5 34.1 - + + -
122A LEU* 4.0 3.1 - - + -
125A LEU* 4.1 15.5 - - + -
136A VAL* 3.5 30.1 - - + -
137A VAL* 1.3 72.6 - - - +
139A CYS* 1.3 61.4 + - - +
140A MET* 3.7 18.1 + - + -
155A PHE* 3.6 38.1 - + - -
171A PHE* 4.5 1.3 - - + -
172A ALA 3.0 9.6 + - - -
173A VAL* 3.5 26.9 - - + +
174A PHE* 2.8 28.8 + - - +
191A VAL* 4.1 4.7 - - + -
195A LEU* 3.4 25.1 - - + -
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Residues in contact with CYS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A VAL* 4.0 3.8 - - - -
86A PHE 2.8 13.4 + - - +
87A TYR* 3.3 1.6 - - - -
88A GLY 2.7 28.9 + - - -
94A ALA* 3.6 24.1 - - + +
97A PHE* 4.2 8.5 - - - -
98A ALA* 3.8 22.0 - - + -
101A LEU* 3.8 28.9 - - - -
137A VAL* 4.0 0.4 + - - -
138A PHE* 1.3 71.7 - - - +
140A MET* 1.3 54.9 + - - +
174A PHE* 3.3 19.7 - - - +
176A LEU* 4.2 7.4 - - + -
219A PHE* 5.3 0.9 - - - -
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Residues in contact with MET 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PHE 4.3 3.1 - - - +
87A TYR 4.1 3.6 - - - -
88A GLY* 3.5 13.9 - - - -
117A PRO* 5.1 3.6 - - + -
138A PHE* 3.9 27.1 - - + +
139A CYS* 1.3 82.7 - - - +
141A ALA* 1.3 57.8 + - - +
152A ALA* 3.8 15.7 - - + -
155A PHE* 3.7 25.4 - - + -
173A VAL* 5.0 3.4 - - + -
174A PHE 3.0 8.6 + - - +
175A GLY* 3.3 4.7 - - - -
176A LEU* 2.7 31.5 + - - +
185A ASN* 4.3 1.0 + - - -
187A MET* 3.6 42.2 - - + -
188A GLY* 4.4 10.2 + - - +
191A VAL* 4.4 11.7 - - + -
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A GLY* 3.0 22.7 + - - +
140A MET* 1.3 75.1 - - - +
142A THR* 1.3 62.1 + - - +
143A TYR* 4.1 1.3 - - + -
149A THR* 3.5 26.0 + - + +
176A LEU* 3.4 12.6 - - + -
187A MET* 3.9 11.4 - - - +
751A FMN 3.3 40.8 - - - +
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Residues in contact with THR 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ALA* 1.3 71.0 - - - +
143A TYR* 1.3 70.7 + - - +
146A GLY* 3.4 32.3 - - - -
147A ASP 3.6 6.7 - - - +
176A LEU 3.2 9.6 + - - -
185A ASN* 3.4 12.1 + - - -
186A ALA 4.0 8.5 - - - +
187A MET* 3.0 25.8 + - - +
188A GLY 4.2 1.4 + - - -
751A FMN 2.8 58.8 + - + +
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Residues in contact with TYR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLN* 3.0 47.1 - - + +
91A THR* 3.0 20.7 - - + +
141A ALA* 4.1 2.2 + - + -
142A THR* 1.3 91.0 - - - +
144A GLY* 1.3 67.8 + - - +
145A GLU 3.8 0.2 - - - -
146A GLY 3.2 3.3 + - - -
147A ASP* 2.7 36.4 + - + +
148A PRO 4.8 7.6 - - - +
149A THR* 3.5 18.8 - - + -
517A ARG* 5.5 3.4 - - - +
751A FMN 2.9 97.2 + + + +
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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