Contacts of the strand formed by residues 129 - 137 (chain A) in PDB entry 3FBK
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 GLY 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A GLN* 3.2 29.2 + - - -
119A TRP* 3.4 5.8 - - - -
120A ASN* 2.8 39.8 + - - +
127A GLN 3.3 1.0 + - - -
128A SER* 1.3 72.9 - - - +
130A LEU* 1.3 62.3 + - - -
76B PRO* 6.1 0.7 - - - -
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Residues in contact with LEU 130 (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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61A LYS* 4.4 21.7 + - - +
117A THR* 3.9 26.0 - - + +
118A VAL 3.9 1.1 - - - -
119A TRP* 3.8 21.9 - - + -
129A GLY* 1.3 72.0 - - - -
131A ILE* 1.3 63.1 + - - +
132A GLY* 3.4 27.4 - - - +
133A CYS* 4.9 4.9 - - - -
156A GLY* 5.6 0.2 - - - -
157A GLU* 4.0 33.9 - - + +
76B PRO* 3.9 32.1 - - + +
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Residues in contact with ILE 131 (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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34A ALA* 2.9 36.7 - - + +
58A LEU* 4.5 5.4 - - + -
59A ILE 3.4 22.5 - - - +
60A SER* 4.2 13.2 - - - +
61A LYS* 5.9 1.7 - - - +
66A CYS* 4.1 16.4 - - - -
68A PRO* 4.1 10.5 - - + -
118A VAL* 2.9 36.8 + - + +
119A TRP 3.9 2.5 - - - +
120A ASN* 3.8 36.6 - - + +
130A LEU* 1.3 77.0 - - - +
132A GLY* 1.3 60.6 + - - +
154A LEU* 4.5 5.8 - - + -
155A LEU 4.7 0.3 - - - +
156A GLY* 5.9 0.7 - - - -
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Residues in contact with GLY 132 (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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34A ALA* 4.3 0.7 - - - -
117A THR* 3.6 1.6 - - - +
118A VAL* 2.9 29.0 + - - +
130A LEU* 3.4 9.5 - - - +
131A ILE* 1.3 82.2 - - - +
133A CYS* 1.3 62.2 + - - +
154A LEU* 4.0 19.7 - - - -
155A LEU 3.3 13.0 - - - -
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Residues in contact with CYS 133 (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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115A LEU* 4.2 9.9 - - + -
116A VAL 3.2 15.0 - - - +
117A THR* 3.5 17.7 - - + +
130A LEU* 4.9 5.4 - - - -
132A GLY* 1.3 76.5 - - - +
134A MSE 1.3 63.5 + - - +
154A LEU* 4.3 5.1 - - - -
155A LEU* 2.8 38.4 + - - +
156A GLY 3.5 21.8 - - - -
157A GLU* 4.1 15.7 - - - -
160A GLY* 3.5 15.9 - - - -
161A ARG* 4.2 4.3 - - - -
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Residues in contact with MSE 134 (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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37A LEU* 3.9 19.3 - - + -
39A LEU* 4.0 12.3 - - - -
115A LEU* 3.6 3.1 - - - +
116A VAL* 2.9 40.0 + - + +
133A CYS* 1.3 77.6 - - - +
135A SER* 1.3 61.0 + - - +
136A PHE* 3.8 22.4 - - + -
152A TYR* 3.5 31.2 - - + -
153A TYR 3.4 27.8 - - - +
154A LEU* 3.7 23.8 - - + -
155A LEU* 5.1 1.1 - - + -
160A GLY* 3.0 12.8 - - - -
163A LYS 3.7 7.4 - - - +
164A HIS* 4.2 8.7 - - + -
165A LEU 6.0 0.2 - - - -
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Residues in contact with SER 135 (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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75A ILE* 5.1 0.4 - - - -
113A ARG* 2.9 45.0 + - - -
114A LEU 3.0 15.0 - - - -
115A LEU* 4.2 6.5 - - - -
134A MSE 1.3 75.0 - - - +
136A PHE* 1.3 66.7 - - - +
160A GLY 2.8 20.0 + - - -
161A ARG* 3.1 12.6 - - - -
163A LYS 3.0 6.7 + - - +
164A HIS* 3.0 24.1 + - - +
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Residues in contact with PHE 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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39A LEU* 4.4 4.5 - - + -
41A ILE* 3.8 22.4 - - + -
113A ARG* 3.3 3.7 - - - -
114A LEU* 2.7 45.8 + - + +
116A VAL* 4.3 10.8 - - + -
134A MSE 3.8 37.2 - - + -
135A SER* 1.3 73.4 - - - +
137A GLY* 1.3 63.5 + - - +
141A LEU* 4.1 22.9 - - + -
146A LYS* 5.1 0.4 - - - -
148A ILE* 3.5 42.2 - - + -
152A TYR* 4.1 6.1 - + - -
164A HIS* 3.2 40.8 - + + -
201A SO4 3.7 5.8 - - - +
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Residues in contact with GLY 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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112A LYS 4.0 5.6 - - - -
113A ARG* 3.6 16.5 - - - +
136A PHE* 1.3 72.5 - - - +
138A VAL* 1.3 65.1 + - - -
139A LYS 3.4 2.5 - - - -
140A SER* 3.4 7.8 + - - -
141A LEU* 3.1 22.2 + - - +
201A SO4 2.9 22.9 + - - -
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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