Contacts of the strand formed by residues 108 - 114 (chain A) in PDB entry 1X9L
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 HIS 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ALA* 4.2 7.0 - - + -
47A ALA 4.1 9.9 - - - +
74A LEU* 4.0 1.2 - - - +
75A MET* 2.7 45.3 + - + +
77A THR* 4.6 0.4 - - + -
86A MET* 3.8 17.3 - - + -
92A LEU* 5.5 2.2 - - - +
102A LEU* 3.9 15.0 - - - -
103A GLN 3.0 26.5 + - - +
104A ARG 2.9 23.6 + - - -
105A ASP* 4.1 2.0 - - - -
106A GLY 4.4 0.4 - - - -
107A ASP* 1.3 87.9 + - - +
109A VAL* 1.3 65.5 + - - +
110A MET* 3.3 24.9 - - + +
150A CU1 2.1 31.8 - - - -
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Residues in contact with VAL 109 (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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46A ALA* 3.1 4.3 - - - +
47A ALA* 3.0 39.4 + - + +
49A MET* 5.3 4.7 - - + -
61A LEU* 5.2 4.0 - - + -
64A ALA* 3.8 19.5 - - + -
72A PRO 4.6 0.7 - - - -
73A MET 3.5 17.9 - - - +
74A LEU* 3.8 25.1 - - + +
92A LEU* 5.7 0.9 - - + -
102A LEU* 4.1 18.2 - - + +
108A HIS* 1.3 79.2 - - - +
110A MET* 1.3 61.5 + - - +
111A LEU* 3.4 27.2 + - + -
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Residues in contact with MET 110 (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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44A ASP* 5.1 13.0 - - + +
45A THR* 3.3 17.9 - - - +
46A ALA* 4.8 2.2 - - + -
71A SER 3.1 1.2 - - - +
73A MET* 2.7 42.6 + - + +
75A MET* 3.3 24.0 - - + +
86A MET* 4.4 7.6 - - + +
104A ARG* 5.6 3.4 - - + +
108A HIS* 3.3 13.4 + - + +
109A VAL* 1.3 68.5 - - - +
111A LEU* 1.3 60.8 + - - +
112A MET* 2.9 23.6 + - + +
150A CU1 2.4 30.7 - - - -
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A VAL* 3.4 41.1 - - + -
44A ASP* 4.5 0.3 - - - -
45A THR* 3.0 37.9 + - + +
47A ALA* 4.2 14.8 - - + +
64A ALA* 3.8 25.8 - - + +
66A THR* 4.3 15.3 - - + -
68A LEU* 5.3 2.2 - - + -
69A ALA* 3.3 22.0 - - + +
72A PRO* 3.9 9.2 - - + -
109A VAL* 3.4 26.8 + - + +
110A MET* 1.3 65.8 - - - +
112A MET* 1.3 60.5 + - - +
113A GLY 4.1 0.2 + - - -
114A LEU 4.8 1.2 + - - -
126A ILE* 5.2 6.5 - - + -
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Residues in contact with MET 112 (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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44A ASP* 3.6 33.0 - - + +
45A THR 4.5 0.7 - - - +
69A ALA* 3.4 1.2 - - - +
70A THR 3.3 2.9 + - - -
71A SER* 2.8 46.0 + - - +
73A MET* 4.2 20.4 - - - +
88A MET* 5.8 1.8 - - - +
110A MET* 2.9 27.4 + - + +
111A LEU* 1.3 71.5 - - - +
113A GLY* 1.3 68.1 + - - +
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Residues in contact with GLY 113 (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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43A ARG* 4.2 14.3 + - - -
44A ASP* 4.2 7.1 - - - +
70A THR* 2.7 41.7 + - - -
71A SER* 4.7 2.5 - - - -
112A MET* 1.3 79.8 - - - +
114A LEU* 1.3 63.1 + - - +
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Residues in contact with LEU 114 (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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38A VAL* 3.4 34.3 - - + +
43A ARG* 2.7 66.6 + - + +
45A THR* 5.0 4.7 - - + -
68A LEU* 3.6 19.7 - - + +
69A ALA* 4.2 4.0 - - - +
70A THR* 4.6 0.6 + - - -
111A LEU 4.8 0.8 + - - -
112A MET 3.7 0.8 - - - -
113A GLY* 1.3 74.2 - - - +
115A LYS* 1.3 60.5 + - - +
116A ARG 2.9 31.4 - - - +
117A PRO* 5.9 0.7 - - + -
118A LEU* 3.7 28.0 - - + -
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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