Contacts of the strand formed by residues 42 - 52 (chain A) in PDB entry 5CS9
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 PHE 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A THR 3.5 19.3 - - - -
39A ILE* 3.5 21.8 - - - +
40A HIS* 3.1 7.7 - - - +
41A GLU* 1.3 85.5 - - + +
43A LYS* 1.3 61.0 + - - +
44A LYS* 3.6 3.6 + - - +
71A ALA* 3.8 13.0 - - + -
74A CYS* 3.8 28.7 - - + -
75A THR* 3.4 28.0 - - - -
86A ALA* 5.1 0.4 - - - -
87A PHE* 3.6 24.2 - + - -
119A TYR* 3.9 24.6 - - + -
120A GLU 3.1 7.4 - - - +
121A ASN* 3.5 33.4 - - + -
122A LYS* 4.2 6.8 - - - -
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Residues in contact with LYS 43 (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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42A PHE* 1.3 71.2 - - - +
44A LYS* 1.3 64.3 + - - +
45A SER* 3.8 5.5 + - - +
104A MET* 4.8 4.4 - - - +
118A LEU 3.6 1.2 - - - +
119A TYR* 3.5 2.8 - - - -
120A GLU* 2.7 45.0 + - + +
122A LYS* 4.4 2.5 - - + +
125A ILE* 3.7 31.4 - - + -
137A LYS* 2.9 29.3 + - - +
139A THR* 3.6 25.1 - - + -
171A ASP* 2.6 33.6 + - - -
173A GLN* 4.1 8.7 - - - +
176A TYR* 3.7 25.1 - - - +
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Residues in contact with LYS 44 (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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42A PHE 3.6 4.7 + - - +
43A LYS* 1.3 72.1 - - - +
45A SER* 1.3 66.4 + - - +
46A ALA* 4.2 10.8 + - - +
117A ASP* 4.0 20.9 + - + -
118A LEU 3.4 6.7 - - - +
119A TYR* 3.8 41.0 + - + -
173A GLN* 2.9 23.2 - - - +
174A GLU* 5.3 1.6 - - - +
176A TYR* 4.7 3.6 + - - -
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Residues in contact with SER 45 (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 LYS* 3.8 7.1 + - - -
44A LYS* 1.3 74.5 + - - +
46A ALA* 1.3 67.8 + - - +
48A THR* 3.4 17.9 + - - -
110A LYS* 5.1 9.0 + - - -
117A ASP* 4.8 0.2 - - - -
118A LEU* 2.8 47.6 + - - +
120A GLU* 4.4 11.6 + - - -
171A ASP* 5.3 0.2 + - - -
173A GLN* 3.8 18.7 + - - +
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Residues in contact with ALA 46 (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 LYS* 4.0 15.8 + - + +
45A SER* 1.3 73.3 - - - +
47A LYS* 1.3 68.5 + - + +
48A THR* 2.6 21.7 + - - -
117A ASP* 3.4 13.0 - - - +
173A GLN* 5.8 0.4 - - - -
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Residues in contact with LYS 47 (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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46A ALA* 1.3 80.4 - - + +
48A THR* 1.3 58.1 + - - +
91A LYS* 6.1 1.3 - - - +
112A PHE* 3.5 44.1 - - + -
113A GLY 2.9 31.7 + - - +
114A HIS* 4.5 18.9 - - - +
116A PHE 3.0 18.1 + - - -
117A ASP* 3.2 3.6 + - - +
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Residues in contact with THR 48 (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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45A SER* 3.4 19.3 + - - -
46A ALA 2.6 21.6 + - - -
47A LYS* 1.3 77.4 + - - +
49A THR* 1.3 73.5 + - - +
88A VAL* 4.1 0.5 - - - +
110A LYS* 3.8 30.0 + - + -
111A GLU 3.4 10.8 - - - +
112A PHE* 5.4 0.2 - - - -
113A GLY 5.0 0.2 - - - -
116A PHE* 3.2 15.8 + - - +
117A ASP 3.6 0.7 - - - -
118A LEU* 3.3 33.8 + - + +
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Residues in contact with THR 49 (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 THR* 1.3 79.8 - - - +
50A LEU* 1.3 80.5 + - - +
51A ILE* 4.9 4.7 - - + -
88A VAL* 3.7 20.6 - - - +
97A LEU* 4.4 8.5 - - - +
99A PHE* 4.8 0.2 - - - -
110A LYS* 3.3 5.9 - - - +
111A GLU* 2.9 49.5 + - + +
112A PHE 5.1 2.0 - - - +
116A PHE* 3.8 36.5 - - + -
118A LEU* 5.2 0.2 - - - -
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Residues in contact with LEU 50 (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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49A THR* 1.3 89.4 + - - +
51A ILE* 1.3 63.0 + - - +
52A LYS 4.1 1.0 + - - -
86A ALA* 4.9 0.2 - - + -
88A VAL* 4.2 2.4 - - - +
97A LEU* 5.7 0.9 - - - +
99A PHE* 4.0 34.2 - - + -
101A PHE* 4.1 13.9 - - + +
102A ASN* 3.8 29.2 - - - +
103A SER* 3.8 25.8 - - - +
108A VAL* 4.5 5.4 - - + -
109A LYS 3.4 3.1 - - - +
110A LYS* 3.8 26.2 - - + +
118A LEU* 3.8 29.8 - - + -
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Residues in contact with ILE 51 (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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49A THR* 4.9 5.8 - - + -
50A LEU* 1.3 75.5 - - - +
52A LYS* 1.3 73.8 + - + +
53A ILE* 3.7 3.3 + - + +
101A PHE* 5.6 0.4 - - - -
108A VAL* 3.4 4.1 - - - -
109A LYS* 2.8 55.6 + - + +
111A GLU* 3.1 44.0 - - + +
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Residues in contact with LYS 52 (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 LEU 4.1 1.0 + - - -
51A ILE* 1.3 83.9 - - + +
53A ILE* 1.3 61.1 + - - +
54A ASP 3.5 17.9 - - - +
55A PRO* 3.3 25.5 + - + +
57A LEU* 3.0 31.1 + - + +
58A LYS* 5.1 0.4 - - - +
59A ILE* 3.8 31.4 - - + +
101A PHE* 4.3 19.0 - - + -
107A GLY 3.5 7.4 - - - +
108A VAL* 4.5 2.0 - - - +
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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