Contacts of the strand formed by residues 104 - 112 (chain A) in PDB entry 1ML0
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 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PRO* 3.6 28.7 - - + +
103A ASP* 1.3 96.5 - - + +
105A VAL* 1.3 63.4 + - - +
157A ASP* 3.9 29.2 - - + +
158A ILE 3.6 13.9 - - - +
159A PRO* 4.7 8.7 - - + -
160A LYS* 4.1 10.8 - - - -
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Residues in contact with VAL 105 (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 PRO* 5.0 0.9 - - - -
104A LEU* 1.3 73.9 - - - +
106A ARG* 1.3 62.0 + - - +
107A VAL* 3.4 23.8 + - + -
157A ASP* 3.3 3.4 - - - -
158A ILE* 2.9 44.7 + - + +
160A LYS* 3.9 25.4 - - + +
163A VAL* 3.9 25.4 - - + -
186A ILE* 4.4 6.3 - - + -
187A PRO* 3.8 28.5 - - + +
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Residues in contact with ARG 106 (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 HIS 3.0 18.6 + - - -
36A CYS 2.9 35.5 - - - +
37A LEU* 3.6 16.9 + - - +
38A THR 3.1 11.3 + - - -
39A PRO* 3.7 18.6 - - - +
40A ALA 3.5 23.2 + - - +
41A GLU* 2.6 37.7 + - - +
42A THR* 4.4 2.2 - - - +
43A GLU 5.0 0.6 + - - -
104A LEU 4.2 0.6 + - - -
105A VAL* 1.3 73.2 - - - +
107A VAL* 1.3 60.2 + - - +
108A LEU 4.1 0.7 + - - -
155A MET* 3.6 38.3 - - + +
156A ILE 3.7 3.6 - - - +
157A ASP* 2.8 43.8 + - - +
187A PRO* 3.9 6.4 - - - +
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Residues in contact with VAL 107 (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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105A VAL* 3.4 29.8 + - + -
106A ARG* 1.3 74.0 - - - +
108A LEU* 1.3 62.9 + - - +
109A VAL* 4.2 10.0 + - + -
130A LEU* 4.8 5.4 - - + -
155A MET* 3.7 3.5 - - - -
156A ILE* 3.1 47.5 + - + +
158A ILE* 3.9 13.7 - - + -
163A VAL* 4.9 7.2 - - + -
184A VAL* 4.7 5.8 - - + -
185A MET 3.3 17.7 - - - +
186A ILE* 4.1 17.3 - - + -
187A PRO* 4.5 0.7 - - - -
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Residues in contact with LEU 108 (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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32A ILE* 5.1 0.2 - - + -
36A CYS* 3.9 34.8 - - + +
37A LEU* 3.9 21.9 - - + +
47A CYS* 4.8 1.3 - - - -
51A LEU* 5.5 2.0 - - + -
62A LEU* 4.2 21.5 - - + -
106A ARG 4.1 0.8 + - - -
107A VAL* 1.3 74.1 - - - +
109A VAL* 1.3 62.0 + - - +
110A VAL* 5.5 0.2 - - + -
145A VAL* 4.8 4.5 - - + -
153A VAL* 4.1 14.1 - - + -
154A TRP 3.4 16.4 - - - +
155A MET* 4.0 14.8 - - + -
183A THR 3.8 0.5 - - - +
184A VAL* 3.5 2.4 - - - +
185A MET* 2.7 67.4 + - + +
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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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107A VAL* 4.7 14.8 - - + +
108A LEU* 1.3 78.8 - - - +
110A VAL* 1.3 67.1 + - - +
128A VAL* 3.9 28.3 - - + -
130A LEU* 4.9 5.4 - - + -
139A LEU* 4.1 24.2 - - + -
152A THR 3.7 0.5 - - - +
153A VAL* 3.3 7.6 - - - +
154A TRP* 2.9 50.9 + - + +
156A ILE* 5.1 0.2 - - + -
182A VAL* 4.1 8.5 - - + -
183A THR 3.2 10.5 - - - +
184A VAL* 4.6 12.3 - - + -
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Residues in contact with VAL 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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62A LEU* 4.3 15.9 - - + -
109A VAL* 1.3 82.2 - - - +
111A ALA* 1.3 64.3 + - - +
112A GLU* 4.1 16.1 - - + +
151A MET* 4.0 25.6 - - + -
152A THR 3.3 8.7 - - - +
153A VAL* 4.1 15.9 - - + -
181A LYS 3.7 1.6 - - - +
182A VAL* 3.1 4.6 - - - -
183A THR* 2.7 52.5 + - + +
185A MET* 4.7 13.9 - - - -
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Residues in contact with ALA 111 (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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110A VAL* 1.3 72.4 - - - +
112A GLU* 1.3 63.6 + - - +
124A PHE* 3.7 5.5 - - + -
126A ALA* 3.7 24.9 - - + -
128A VAL* 4.2 8.5 - - + -
151A MET* 3.3 2.3 - - - +
152A THR* 2.9 32.5 + - - +
154A TRP* 3.6 24.8 - - + -
173A PHE* 4.8 1.6 - - + -
181A LYS 3.5 5.4 - - - -
182A VAL* 4.4 7.4 - - + +
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Residues in contact with GLU 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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60A HIS* 4.6 18.2 + - - -
63A GLN* 5.3 3.8 + - - -
110A VAL* 4.1 16.5 - - + +
111A ALA* 1.3 77.2 - - - +
113A SER* 1.3 66.7 + - - +
124A PHE* 3.8 10.4 - - - -
150A TYR 3.2 17.0 - - - +
151A MET* 3.8 17.2 - - + +
173A PHE* 4.6 2.0 - - - -
179A GLY 5.2 0.2 - - - +
180A ALA* 3.1 3.5 - - - +
181A LYS* 2.7 78.1 + - + +
183A THR* 5.6 1.2 + - - +
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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