Contacts of the strand formed by residues 125 - 133 (chain B) in PDB entry 5F2R
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 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B GLY* 6.1 4.3 - - - +
101B ARG 3.8 15.3 - - - +
102B THR* 4.9 1.6 - - + -
103B TRP* 3.7 5.6 - - - +
120B VAL 3.3 1.6 - - - +
121B GLU* 3.5 3.1 - - - -
122B LYS 2.8 32.7 + - - +
123B LYS* 3.8 14.6 - - + +
124B THR* 1.3 86.7 - - - +
126B PRO* 1.4 68.2 - - + +
127B TYR* 3.3 26.9 + - + -
141B ALA* 4.7 1.1 - - - -
142B PRO* 4.9 3.1 - - + -
143B GLU* 2.6 38.1 + - - -
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Residues in contact with PRO 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 4.1 22.1 - - + +
101B ARG 3.2 22.2 - - - +
103B TRP* 3.7 12.9 - - + +
108B VAL* 3.8 30.1 - - + -
119B VAL* 3.5 21.3 - - + +
120B VAL 3.6 5.8 - - - +
125B LYS* 1.4 83.4 - - + +
127B TYR* 1.3 66.3 + - - +
128B ILE* 4.0 3.3 - - - +
142B PRO* 3.2 26.9 - - + +
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Residues in contact with TYR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL* 3.2 4.7 - - - -
120B VAL* 2.8 41.0 + - + +
122B LYS* 3.4 52.8 - - + -
123B LYS* 4.3 16.4 - - + +
125B LYS* 3.9 23.5 + - + -
126B PRO* 1.3 74.1 - - - +
128B ILE* 1.3 61.3 + - - +
139B THR* 3.4 34.8 - - + -
140B PHE 3.4 5.4 - - - -
141B ALA* 3.5 38.4 - - + +
142B PRO* 4.5 0.4 - - - -
144B GLU* 4.2 6.1 - - - -
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Residues in contact with ILE 128 (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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92B VAL* 3.8 26.9 - - + -
95B ALA* 5.0 4.3 - - + -
98B LEU* 4.1 12.3 - - + -
117B PHE* 3.5 40.8 - - + -
118B LYS 3.4 3.4 - - - +
119B VAL* 4.4 1.8 - - + -
126B PRO 4.0 8.3 - - - +
127B TYR* 1.3 74.1 - - - +
129B GLN* 1.3 62.0 + - - +
130B VAL* 4.2 10.0 + - + -
138B LYS 3.7 1.0 - - - +
139B THR* 3.2 2.8 - - - -
140B PHE* 2.8 52.4 + - + +
142B PRO* 3.9 27.1 - - + -
145B ILE* 4.2 14.6 - - + -
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Residues in contact with GLN 129 (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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89B GLU 4.5 1.6 - - - +
118B LYS* 2.8 64.0 + - + +
120B VAL* 3.7 30.2 - - + +
127B TYR 4.0 0.4 + - - -
128B ILE* 1.3 72.3 - - - +
130B VAL* 1.3 68.8 + - - +
137B THR* 3.4 31.8 - - + +
138B LYS 3.3 5.2 - - - +
139B THR* 3.9 12.5 + - - +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.9 28.9 - - + -
89B GLU 3.6 18.8 - - - +
90B ASN* 3.7 15.5 - - + +
92B VAL* 3.9 24.7 - - + -
117B PHE* 4.7 0.9 - - + -
118B LYS* 6.1 0.2 - - - -
128B ILE* 4.2 6.1 - - + +
129B GLN* 1.3 81.4 - - - +
131B ASP* 1.3 61.8 + - - +
132B ILE* 3.6 4.4 + - + -
137B THR* 3.4 7.0 - - - +
138B LYS* 2.8 34.6 + - - +
140B PHE* 3.9 21.5 - - + -
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Residues in contact with ASP 131 (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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68B PHE* 3.7 11.3 - - - +
69B THR 5.1 0.7 - - - +
70B PRO* 6.4 0.7 - - - -
90B ASN* 3.0 36.2 - - - +
130B VAL* 1.3 71.6 - - - +
132B ILE* 1.3 60.6 + - - +
133B GLY* 2.6 31.8 + - - -
134B GLY 4.8 0.2 - - - -
135B GLY* 3.1 34.4 + - - -
136B GLN 3.3 10.5 - - - +
137B THR* 4.4 3.8 - - - +
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Residues in contact with ILE 132 (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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68B PHE* 3.9 33.3 - - + +
69B THR 3.7 5.1 - - - +
72B GLY* 3.1 23.6 - - - +
130B VAL* 4.2 4.3 - - + +
131B ASP* 1.3 73.5 - - - +
133B GLY* 1.3 57.8 + - - +
136B GLN* 2.8 29.9 + - + +
138B LYS* 3.6 51.1 - - + +
140B PHE* 4.2 10.3 - - + -
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Residues in contact with GLY 133 (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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69B THR 3.8 6.5 + - - -
70B PRO* 3.4 16.8 - - - -
71B GLU 5.5 0.2 - - - -
72B GLY* 4.1 4.9 - - - -
131B ASP* 2.6 15.5 + - - -
132B ILE* 1.3 74.4 - - - +
134B GLY* 1.3 66.2 + - - -
135B GLY 3.1 3.2 + - - -
136B GLN* 3.1 22.0 + - - +
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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