Contacts of the strand formed by residues 128 - 138 (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 LYS 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A LEU* 4.6 27.8 + - + +
64A VAL 4.5 4.0 - - - +
65A SER 5.9 0.2 - - - +
66A PRO* 5.1 0.4 - - - -
123A VAL* 3.3 18.5 + - + +
124A VAL* 2.9 39.1 + - + +
127A GLU* 1.3 106.6 + - + +
129A VAL* 1.3 61.4 + - - +
172A VAL* 4.6 20.2 - - + -
71C THR* 4.9 14.8 - - - +
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Residues in contact with VAL 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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63A LEU* 3.6 7.6 - - - +
64A VAL* 3.2 40.8 + - + +
66A PRO* 3.7 30.7 - - + -
71A ALA 5.5 3.4 - - - +
72A THR 5.4 0.2 - - - -
73A GLU 3.5 29.2 - - - +
74A GLY* 3.7 7.9 - - - -
75A ILE* 5.5 5.2 - - + +
121A LEU 4.1 0.9 - - - +
122A CYS* 3.7 24.7 - - + -
123A VAL* 4.3 5.8 - - - +
124A VAL 5.2 1.1 - - - +
128A LYS* 1.3 76.0 - - - +
130A TRP* 1.3 69.0 + - - +
131A GLN* 5.8 0.7 - - + -
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Residues in contact with TRP 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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61A CYS* 3.4 27.8 - - - -
62A GLU 3.3 22.9 - - - -
63A LEU* 3.6 28.5 - - + +
74A GLY* 3.4 24.3 - - - -
75A ILE 3.7 1.2 + - - -
121A LEU* 3.1 47.4 + - + +
123A VAL* 3.6 18.0 - - + +
129A VAL* 1.3 82.0 - - - +
131A GLN* 1.3 60.1 + - - +
162A ARG* 3.2 32.8 - - + +
163A PRO* 3.2 49.6 - - + -
165A VAL* 3.6 23.3 - - + +
174A LEU* 5.9 1.1 - - + -
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Residues in contact with GLN 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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61A CYS* 3.3 3.9 - - - -
62A GLU* 2.9 43.1 + - - +
64A VAL* 3.7 39.7 - - + +
75A ILE* 3.7 27.6 + - + +
77A PHE* 3.7 31.7 - - - +
129A VAL* 4.7 1.1 - - + +
130A TRP* 1.3 76.4 - - - +
132A ILE* 1.3 65.8 + - - +
133A ARG* 3.9 11.6 + - - +
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Residues in contact with ILE 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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59A VAL* 3.9 24.7 - - + -
60A SER 3.7 3.1 - - - +
61A CYS* 3.6 20.6 - - + -
75A ILE 3.0 11.1 + - - +
76A LEU* 3.5 12.6 - - + +
77A PHE* 2.9 26.0 + - - +
78A PHE* 5.5 0.2 - - - -
116A ILE* 4.5 16.4 - - + -
121A LEU* 3.7 27.6 - - + -
131A GLN* 1.3 73.9 - - - +
133A ARG* 1.3 61.1 + - - +
134A VAL* 4.1 13.1 + - + +
157A LEU* 4.9 7.2 - - + -
160A PHE* 5.3 0.9 - - + -
162A ARG* 6.2 1.3 - - - -
185A LEU* 3.7 29.2 - - + -
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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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58A GLN 4.1 0.7 - - - +
59A VAL* 3.7 0.7 - - - -
60A SER* 2.9 48.2 + - - +
77A PHE* 3.2 38.0 - - + +
79A ASN* 3.4 27.9 - - + +
131A GLN* 3.9 16.0 + - - +
132A ILE* 1.3 71.7 - - - +
134A VAL* 1.3 63.6 + - - +
135A ASP* 3.5 21.4 + - - +
85D GLY* 3.7 23.5 - - - +
86D LEU* 3.9 25.3 - - - +
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Residues in contact with VAL 134 (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 3.4 7.4 - - - +
59A VAL* 3.7 22.4 - - + -
76A LEU* 6.4 0.2 - - + -
77A PHE 3.0 9.0 + - - +
78A PHE* 3.5 30.2 - - + -
79A ASN 3.0 21.1 + - - -
106A MET* 3.8 19.5 - - + -
132A ILE* 4.1 14.6 - - + -
133A ARG* 1.3 77.2 - - - +
135A ASP* 1.3 70.3 + - - +
136A LEU* 5.1 6.7 - - + -
153A ALA* 5.3 3.8 - - + -
156A ALA* 6.1 0.7 - - + -
157A LEU* 3.7 21.1 - - + -
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Residues in contact with ASP 135 (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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56A LEU 3.8 0.7 - - - +
57A GLY* 3.5 3.1 - - - -
58A GLN* 2.9 37.9 + - + +
60A SER* 5.3 1.9 + - - -
79A ASN* 3.3 24.3 - - - +
133A ARG* 3.5 18.8 + - - +
134A VAL* 1.3 82.7 - - - +
136A LEU* 1.3 63.2 + - - +
137A HIS* 4.2 13.9 - - + +
83D LYS 2.9 28.7 - - - +
84D ILE* 3.6 4.5 - - - +
85D GLY 3.4 20.2 + - - +
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Residues in contact with LEU 136 (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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55A VAL* 4.6 4.5 - - + -
56A LEU 3.3 3.4 - - - +
57A GLY* 3.7 19.1 - - - -
58A GLN 4.8 0.4 - - - +
79A ASN 2.9 8.2 + - - +
80A LEU* 3.4 16.1 - - + +
81A GLU* 3.2 25.6 + - - +
106A MET* 3.7 37.7 - - + -
134A VAL* 5.1 4.5 - - + -
135A ASP* 1.3 83.0 - - - +
137A HIS* 1.3 65.4 + - - +
149A ALA* 3.4 36.8 - - + +
152A ALA* 4.1 14.4 - - + -
153A ALA* 4.1 12.1 - - + +
156A ALA* 5.6 1.6 - - + -
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Residues in contact with HIS 137 (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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55A VAL* 3.5 6.7 - - - +
56A LEU* 2.9 45.4 + - + -
58A GLN* 5.9 0.9 - - + -
80A LEU* 5.2 0.2 - - - -
81A GLU* 3.7 19.7 + - + +
83A SER* 5.3 5.1 - - - -
135A ASP* 4.2 14.9 - - + +
136A LEU* 1.3 79.4 + - - +
138A LEU* 1.3 60.8 + - - +
139A LEU* 3.3 19.7 - - + +
81D ARG* 4.5 17.4 + - - -
82D PRO 4.2 6.7 - - - -
83D LYS* 3.5 28.6 + - + -
85D GLY 5.7 2.2 - - - -
121D GLN* 3.3 37.2 + - - +
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Residues in contact with LEU 138 (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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53A THR* 4.7 3.8 - - + -
54A ARG 4.1 0.4 - - - +
55A VAL* 3.8 20.6 - - + -
80A LEU* 4.9 4.7 - - + +
81A GLU 3.6 7.5 + - - +
82A LEU* 3.7 35.2 - - + -
83A SER* 3.3 23.2 + - - +
86A ALA* 3.5 23.8 - - + +
90A PHE* 4.2 10.3 - - + -
136A LEU 4.1 0.6 + - - -
137A HIS* 1.3 70.7 - - - +
139A LEU* 1.3 59.8 + - - +
140A ASN 3.8 18.4 - - - +
141A HIS* 4.2 8.1 - - + -
145A ILE* 3.7 42.0 - - + -
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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