Contacts of the strand formed by residues 121 - 129 (chain C) in PDB entry 6XHU
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 SER 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A THR* 3.5 21.6 - - - +
305A PHE 3.9 11.4 + - - -
306A GLN 5.7 0.3 + - - -
28C ASN* 4.2 0.2 + - - -
117C CYS* 3.3 4.2 - - - -
118C TYR 3.0 32.9 + - - +
119C ASN* 3.9 6.9 + - - +
120C GLY* 1.3 81.5 + - - +
122C PRO* 1.3 71.6 - - - +
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Residues in contact with PRO 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A PRO* 3.7 21.2 - - + +
304A THR* 4.4 0.7 - - - -
305A PHE* 3.3 37.8 + - - +
306A GLN 5.6 3.4 - - - +
14C GLU* 3.9 33.2 - - + +
17C MET* 5.2 1.8 - - + -
115C LEU* 3.9 19.5 - - + -
116C ALA 3.8 5.8 - - - +
117C CYS* 3.8 6.5 - - - -
120C GLY 4.2 4.0 - - - +
121C SER* 1.3 87.0 - - - +
123C SER* 1.3 59.2 + - - +
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Residues in contact with SER 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A MET* 4.7 9.8 - - - +
7A ALA 4.5 0.5 - - - +
8A PHE* 5.0 0.9 - - - -
9A PRO* 4.1 6.4 - - - +
298A ARG* 4.7 10.6 + - - -
299A GLN* 6.0 1.6 - - - -
302A GLY* 4.4 3.6 - - - -
303A VAL 2.8 26.9 + - - -
304A THR* 4.2 2.5 - - - +
305A PHE* 3.5 19.1 - - - -
116C ALA* 2.8 19.1 + - - -
118C TYR* 3.9 27.8 - - - -
122C PRO* 1.3 74.3 - - - +
124C GLY* 1.3 56.2 + - - +
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Residues in contact with GLY 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A MET* 3.5 19.5 - - - -
7A ALA 3.1 13.5 - - - -
9A PRO* 4.2 6.7 - - - +
114C VAL 3.7 0.2 - - - +
115C LEU* 3.6 8.3 - - - +
116C ALA* 2.9 27.3 + - - +
122C PRO 3.9 0.4 - - - -
123C SER* 1.3 81.5 - - - +
125C VAL* 1.3 61.6 + - - -
126C TYR* 5.1 0.2 - - - -
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Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS 4.5 0.5 - - - +
6A MET* 3.6 0.7 - - - +
7A ALA* 2.9 42.9 + - + +
8A PHE 3.8 12.8 - - - +
9A PRO* 4.5 3.4 - - + -
125A VAL* 3.7 25.6 - - + -
7C ALA* 3.7 18.4 - - + +
8C PHE 4.0 10.8 - - - +
10C SER* 4.4 12.8 - - - +
113C SER* 4.2 9.9 - - - -
114C VAL 3.3 13.5 - - - +
115C LEU* 4.4 9.9 - - + -
124C GLY* 1.3 75.3 - - - +
126C TYR* 1.3 66.4 + - - +
150C PHE* 4.7 2.0 - - + -
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Residues in contact with TYR 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ARG* 3.8 33.2 - - + -
5A LYS 4.0 17.3 - - - +
6A MET* 3.4 33.9 - - + -
7C ALA* 4.1 9.4 - - - -
113C SER* 3.3 1.4 - - - -
114C VAL* 2.8 58.2 + - + +
116C ALA* 4.3 7.0 - - + -
125C VAL* 1.3 79.3 - - - +
127C GLN* 1.3 66.9 + - - +
128C CYS* 4.1 5.8 + - - -
138C GLY* 3.6 8.5 - - - -
139C SER* 3.1 28.9 + - - -
140C PHE* 3.5 25.1 - - - -
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Residues in contact with GLN 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ARG* 3.2 20.1 + - - -
5C LYS* 4.1 28.1 + - + +
6C MET 3.5 29.5 + - - +
7C ALA* 3.7 2.0 - - - +
8C PHE* 4.1 6.6 - - - -
111C THR* 3.6 26.3 + - - -
112C PHE 3.4 14.0 - - - +
113C SER* 2.7 29.1 + - - -
126C TYR* 1.3 77.7 - - - +
128C CYS* 1.3 66.2 + - - +
290C GLU 5.0 5.6 + - - +
291C PHE* 6.4 0.9 - - + -
295C ASP* 4.1 5.1 + - - -
298C ARG* 4.1 17.4 - - - +
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Residues in contact with CYS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ARG* 3.4 24.2 - - - +
111C THR* 3.2 7.3 - - - -
112C PHE* 2.9 64.3 + - - +
114C VAL* 4.0 15.0 - - - -
126C TYR* 4.5 6.3 - - + -
127C GLN* 1.3 76.5 - - - +
129C ALA* 1.3 63.7 + - - +
136C ILE* 4.4 16.6 - - + -
137C LYS 4.6 3.4 - - - +
290C GLU* 3.6 9.6 - - - -
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Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C GLY 4.7 0.9 - - - +
110C GLN 3.4 10.3 - - - +
111C THR* 3.9 11.7 - - + -
112C PHE* 4.5 3.8 - - - -
128C CYS* 1.3 76.8 - - - +
130C MET* 1.3 69.1 + - - +
131C ARG* 3.3 15.2 + - - +
136C ILE* 4.0 14.6 - - - +
137C LYS 5.0 0.7 + - - -
200C ILE* 4.4 15.9 - - + -
289C ASP 4.7 0.2 - - - +
290C GLU* 3.2 31.1 + - + +
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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