Contacts of the strand formed by residues 126 - 133 (chain A) in PDB entry 1QFG
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 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ALA* 4.1 6.1 - - - +
58A MET* 4.0 16.3 - - + +
66A VAL* 4.0 14.6 - - + -
106A LEU* 4.5 4.3 - - + -
121A ILE* 3.6 22.9 - - + +
122A ASP 3.8 10.8 - - - +
123A PRO* 3.1 20.9 + - + +
124A TYR 3.3 0.4 - - - -
125A MET* 1.3 88.1 - - - +
127A GLU* 1.3 61.1 + - - +
128A ARG 4.2 7.0 - - - +
129A ALA* 5.2 0.9 - - + -
151A MET* 3.6 39.3 - - + -
152A VAL 3.5 15.3 - - - +
153A SER* 4.6 0.9 - - - -
154A LYS* 3.3 21.7 - - - +
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Residues in contact with GLU 127 (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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54A THR* 4.1 0.5 - - - -
55A ALA* 3.0 35.7 + - + +
58A MET* 4.2 1.1 - - - -
126A LEU* 1.3 74.9 - - - +
128A ARG* 1.3 67.4 + - + +
152A VAL* 2.9 19.2 + - + +
153A SER 3.2 17.9 - - - +
154A LYS* 3.8 6.2 - - + +
155A ARG* 3.1 39.1 + - - +
157A THR* 5.8 0.3 - - - +
193A ARG* 3.7 13.4 + - - +
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Residues in contact with ARG 128 (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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29A ALA* 3.3 24.9 + - - +
30A ALA* 4.4 0.8 - - - +
32A GLN* 2.1 37.2 + - - +
33A SER* 3.8 1.4 - - - +
52A VAL* 3.6 18.7 - - + +
53A VAL 3.3 14.4 - - - +
54A THR* 4.4 10.3 - - - +
58A MET* 3.9 8.1 - - - -
126A LEU* 3.5 5.3 - - - +
127A GLU* 1.3 87.4 - - + +
129A ALA* 1.3 64.3 + - - +
130A GLU* 2.7 34.5 + - + +
151A MET* 3.7 1.7 - - - -
152A VAL* 2.9 43.7 + - + +
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Residues in contact with ALA 129 (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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52A VAL* 3.6 0.3 - - - -
53A VAL* 3.0 36.2 + - + +
58A MET* 5.1 8.5 - - + -
66A VAL* 4.3 23.3 - - + -
69A ALA* 5.4 1.8 - - + -
70A LEU* 4.5 17.5 - - + -
126A LEU* 5.2 0.9 - - + -
128A ARG* 1.3 75.9 - - - +
130A GLU* 1.3 66.8 + - - +
149A LEU* 4.5 3.6 - - + -
150A ASN 3.5 7.4 - - - +
151A MET* 4.3 1.8 - - - +
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Residues in contact with GLU 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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33A SER* 2.4 33.3 + - - -
34A ALA 4.3 1.0 + - - -
35A THR* 2.7 38.8 + - - +
50A ILE* 4.0 3.9 - - + +
51A SER 3.2 12.8 - - - +
52A VAL* 4.3 6.3 - - + -
70A LEU* 5.3 0.7 - - - -
128A ARG* 2.7 40.7 + - + +
129A ALA* 1.3 80.3 - - - +
131A ILE* 1.3 62.2 + - - +
132A MET 4.2 0.2 + - - -
148A LEU* 4.1 0.3 - - - +
149A LEU* 3.6 3.9 - - - +
150A ASN* 2.7 43.3 + - - +
152A VAL* 5.1 6.4 - - + +
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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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50A ILE* 3.5 6.4 - - - +
51A SER* 3.0 36.6 + - - +
70A LEU* 3.3 54.0 - - + +
73A THR* 5.3 3.6 - - + -
76A VAL* 4.0 25.8 - - + -
90A LEU* 4.2 6.3 - - + -
92A ILE* 4.1 20.4 - - + -
130A GLU* 1.3 73.7 - - - +
132A MET* 1.3 66.0 + - - +
133A ARG* 4.0 17.4 + - + +
148A LEU 3.6 10.5 - - - +
149A LEU* 4.1 7.6 - - + -
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Residues in contact with MET 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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35A THR* 4.1 17.0 - - + +
36A GLY* 3.4 29.6 - - - +
46A VAL* 4.8 4.5 - - + -
48A GLN* 4.8 8.7 - - + +
49A SER 3.6 6.5 - - - +
50A ILE* 3.3 46.7 - - + -
130A GLU 4.1 0.8 + - - -
131A ILE* 1.3 72.4 - - - +
133A ARG* 1.3 63.4 + - - +
136A VAL* 3.1 37.7 - - + -
140A TYR* 5.4 0.7 - - - -
147A GLY* 3.0 4.2 - - - -
148A LEU* 2.9 38.0 + - + +
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Residues in contact with ARG 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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48A GLN* 3.6 25.5 + - - +
49A SER* 3.1 30.9 + - - +
50A ILE* 4.1 4.3 - - - +
51A SER* 2.2 44.7 + - - +
73A THR* 3.4 10.7 - - - +
74A PRO* 3.0 32.5 + - - +
75A GLY* 4.5 1.8 - - - -
76A VAL* 6.0 0.4 - - + +
92A ILE* 3.8 20.4 - - + -
93A ARG* 3.6 20.4 + - - +
131A ILE* 4.0 10.6 + - + +
132A MET* 1.3 70.4 - - - +
134A GLY* 1.3 66.6 + - - +
146A GLY 3.5 4.5 - - - +
531A GLN* 4.0 1.9 + - - -
548A THR* 5.8 4.0 - - - +
582A GLU* 3.3 36.0 + - - +
584A GLU* 4.1 0.8 + - - -
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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