Contacts of the strand formed by residues 54 - 64 (chain A) in PDB entry 6H25
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 ARG 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ILE* 4.9 11.9 - - + -
48A VAL 3.4 4.5 - - - +
49A GLU* 3.3 35.5 + - + -
52A LYS* 5.4 0.9 - - - -
53A THR* 1.3 77.8 - - - +
55A VAL* 1.3 64.8 + - - +
138A LEU* 4.1 1.2 - - - +
139A LEU* 3.0 46.4 + - + +
140A ASN* 3.4 14.8 + - + +
37D LEU* 2.6 79.3 + - - +
38D LEU* 3.5 20.9 - - - +
55D LEU* 4.7 4.4 - - - +
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Residues in contact with VAL 55 (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 CYS 3.8 0.7 - - - +
47A ILE* 3.5 4.8 - - - -
48A VAL* 2.9 36.0 + - + +
53A THR* 4.8 2.5 - - + -
54A ARG* 1.3 78.4 - - - +
56A LEU* 1.3 67.4 + - - +
80A LEU* 5.9 1.3 - - + -
136A LEU* 4.6 7.9 - - + -
137A HIS 3.5 11.9 - - - +
138A LEU* 3.8 21.8 - - + -
139A LEU* 5.6 0.4 - - - -
145A ILE* 5.3 3.4 - - + -
148A ALA* 3.7 34.5 - - + +
149A ALA* 4.4 10.1 - - + +
152A ALA* 3.7 23.5 - - + +
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Residues in contact with LEU 56 (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 CYS* 4.1 20.4 - - - -
46A CYS 3.4 16.2 - - - +
47A ILE* 3.7 19.5 - - + +
55A VAL* 1.3 74.0 - - - +
57A GLY* 1.3 62.5 + - - +
58A GLN* 5.7 1.3 - - + -
135A ASP 3.8 0.5 - - - +
136A LEU* 3.3 5.5 - - - +
137A HIS* 2.9 46.9 + - + +
139A LEU* 3.7 23.5 - - + +
83D LYS* 4.8 6.7 - - + -
121D GLN* 4.2 24.2 - - + +
122D VAL 4.3 13.5 - - - +
123D VAL* 4.5 17.9 - - + +
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Residues in contact with GLY 57 (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 GLY 3.2 5.3 - - - +
45A CYS* 3.3 5.0 - - - +
46A CYS* 2.9 49.6 + - - -
55A VAL 4.0 0.6 + - - -
56A LEU* 1.3 78.4 - - - +
58A GLN* 1.3 61.4 + - - +
135A ASP 3.5 5.2 - - - -
136A LEU* 3.7 14.4 - - - -
152A ALA* 4.9 0.4 - - - -
156A ALA* 4.5 3.4 - - - -
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Residues in contact with GLN 58 (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 ASP* 4.7 4.7 + - - +
43A TYR 4.1 9.9 + - - +
44A GLY 3.4 5.5 + - - -
45A CYS* 3.3 18.6 - - - +
56A LEU* 5.7 2.2 - - + -
57A GLY* 1.3 72.8 - - - +
59A VAL* 1.3 88.8 + - - +
60A SER* 4.2 0.6 - - - +
133A ARG 4.1 0.7 - - - +
134A VAL* 3.4 3.6 - - - +
135A ASP* 2.9 38.2 + - + +
136A LEU* 4.8 0.8 - - - +
137A HIS* 5.9 1.1 - - + -
156A ALA* 4.7 0.6 - - - +
83D LYS* 3.0 59.3 + - + +
84D ILE* 3.8 23.7 - - + +
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Residues in contact with VAL 59 (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 GLY 3.4 4.8 + - - +
58A GLN* 1.3 98.3 + - - +
60A SER* 1.3 63.2 + - - +
132A ILE* 3.9 25.4 - - + -
133A ARG 3.7 2.7 - - - -
134A VAL* 3.7 17.9 - - + -
156A ALA* 3.5 38.1 - - + +
157A LEU* 4.2 5.2 - - + -
160A PHE* 3.5 49.3 - - + -
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Residues in contact with SER 60 (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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58A GLN* 4.2 1.4 - - - -
59A VAL* 1.3 78.4 - - - +
61A CYS* 1.3 63.7 + - - +
62A GLU* 5.9 2.4 - - - +
132A ILE* 3.7 1.6 - - - -
133A ARG* 2.9 51.1 + - - +
135A ASP* 5.3 1.4 + - - -
160A PHE* 4.7 2.2 - - - -
84D ILE* 3.7 28.9 - - - +
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Residues in contact with CYS 61 (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 SER* 1.3 78.9 - - - +
62A GLU* 1.3 67.0 + - - +
130A TRP* 3.4 37.2 - - + -
131A GLN 3.3 19.5 - - - -
132A ILE* 3.6 21.5 - - + -
160A PHE* 3.6 27.0 - - + -
162A ARG* 5.0 5.8 - - + -
163A PRO* 5.9 2.8 - - + +
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Residues in contact with GLU 62 (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 SER* 5.9 2.2 - - - +
61A CYS* 1.3 80.2 - - - +
63A LEU* 1.3 72.7 + - - +
64A VAL* 4.0 7.9 - - + +
130A TRP* 3.3 12.2 - - - -
131A GLN* 2.9 45.0 + - - +
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Residues in contact with LEU 63 (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 GLU* 1.3 78.8 - - - +
64A VAL* 1.3 62.5 + - - +
123A VAL* 5.7 4.7 - - + -
128A LYS* 4.6 34.4 + - + +
129A VAL 3.6 9.2 - - - +
130A TRP* 3.6 35.7 - - + -
165A VAL* 5.0 7.0 - - + -
172A VAL* 4.9 13.5 - - + -
174A LEU* 4.4 24.7 - - + -
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Residues in contact with VAL 64 (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 GLU* 4.0 12.3 + - - +
63A LEU* 1.3 79.7 - - - +
65A SER* 1.3 78.7 + - - +
75A ILE* 5.6 5.8 - - + -
127A GLU 4.8 1.1 - - - -
128A LYS* 5.3 2.2 - - - -
129A VAL* 3.2 32.4 + - + +
131A GLN* 3.7 39.7 - - + +
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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