Contacts of the strand formed by residues 107 - 115 (chain C) in PDB entry 4X4S
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 VAL 107 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C LYS* 4.6 7.6 - - + +
24C GLY* 4.7 3.6 - - - -
27C ALA* 3.3 22.2 - - + -
58C LEU* 3.3 41.1 - - + -
60C ILE* 3.8 13.2 - - + -
103C VAL* 3.3 9.3 - - - -
104C VAL 3.1 34.0 + - - +
105C LYS 5.2 0.2 - - - -
106C GLY* 1.3 80.6 - - - +
108C GLU* 1.3 69.2 + - - +
109C VAL* 3.5 19.4 + - + -
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Residues in contact with GLU 108 (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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58C LEU 3.4 21.1 - - - +
59C GLU* 3.7 15.3 - - + -
60C ILE* 2.9 29.3 + - - +
101C HIS* 3.3 31.6 + - + -
102C GLY 3.9 6.4 - - - +
103C VAL* 5.1 5.0 - - - +
106C GLY 5.9 0.4 - - - +
107C VAL* 1.3 76.1 - - - +
109C VAL* 1.3 63.5 + - - +
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Residues in contact with VAL 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 4.0 28.5 - - + -
60C ILE* 3.4 8.7 - - + +
62C VAL* 4.9 4.7 - - + -
87C LEU* 3.5 27.6 - - + +
100C VAL 3.7 1.4 - - - +
101C HIS* 5.4 0.2 - - - -
102C GLY 3.1 32.6 + - - +
104C VAL* 3.9 17.0 - - + -
107C VAL* 3.6 25.1 - - + +
108C GLU* 1.3 80.2 - - - +
110C ASP* 1.3 75.3 + - - +
111C VAL* 4.2 10.8 - - + -
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Residues in contact with ASP 110 (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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59C GLU* 3.1 25.2 - - - +
60C ILE 3.0 7.5 + - - +
61C ASP* 3.8 5.8 - - - +
62C VAL* 2.9 30.8 + - - +
99C TYR* 3.9 12.9 - - + -
100C VAL 3.5 4.0 - - - +
101C HIS* 3.0 24.5 + - - -
109C VAL* 1.3 86.0 + - - +
111C VAL* 1.3 62.3 + - - +
112C VAL* 3.8 3.8 + - + +
37D C 3.5 44.3 + - - +
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Residues in contact with VAL 111 (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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31C LEU* 5.9 0.4 - - + -
35C LEU* 5.6 3.4 - - + -
62C VAL* 3.4 11.0 - - + +
64C LEU* 3.6 37.7 - - + -
79C GLY 4.6 2.0 - - - +
82C ILE* 5.1 1.3 - - + -
83C GLY* 3.9 23.3 - - - +
86C VAL* 5.4 7.4 - - + -
87C LEU* 4.0 34.3 - - + -
99C TYR* 3.7 3.1 - - - -
100C VAL* 3.1 31.6 + - + +
109C VAL* 4.2 6.1 - - + -
110C ASP* 1.3 73.0 - - - +
112C VAL* 1.3 60.5 + - - +
113C PRO* 3.8 3.6 - - - +
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Residues in contact with VAL 112 (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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62C VAL 2.9 8.9 + - - -
63C PHE* 3.2 37.4 - - + +
64C LEU* 2.8 27.8 + - - -
97C HIS* 3.4 35.4 - - + +
98C PRO 4.4 0.9 - - - +
99C TYR* 4.0 9.2 - - + -
110C ASP* 4.4 6.5 - - + +
111C VAL* 1.3 75.1 - - - +
113C PRO* 1.3 64.6 - - + +
127C VAL* 4.0 4.0 - - + -
37D C 3.6 39.5 - - - +
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Residues in contact with PRO 113 (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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64C LEU* 3.8 9.4 - - + +
66C PHE* 4.7 2.7 - - + -
75C LEU* 3.7 32.1 - - + +
76C ARG 4.9 0.2 - - - +
79C GLY* 3.6 30.7 - - - -
80C LEU* 4.3 3.1 - - + +
97C HIS* 2.7 32.4 + - + +
98C PRO* 3.2 35.9 - - + +
99C TYR* 4.2 0.7 - - - -
111C VAL 3.8 6.1 - - - +
112C VAL* 1.3 83.4 - - + +
114C CYS* 1.3 62.9 + - - +
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Residues in contact with CYS 114 (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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63C PHE* 3.5 35.7 - - + -
64C LEU 2.8 21.4 + - - +
65C LEU* 4.1 9.2 - - - -
66C PHE 3.0 23.9 + - - -
75C LEU* 3.6 19.5 - - - +
97C HIS* 5.0 0.4 - - - -
113C PRO* 1.3 75.8 - - - +
115C TYR* 1.3 64.5 + - - +
127C VAL* 4.1 8.3 - - + +
128C ASP* 3.6 13.2 - - - +
131C PRO* 4.1 16.4 - - - -
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Residues in contact with TYR 115 (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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65C LEU* 4.7 0.9 - - - +
66C PHE 3.5 2.0 - - - -
67C PRO 3.1 28.7 - - - -
68C GLU* 3.5 16.2 - - + -
70C PHE* 2.7 33.3 + - + -
71C SER 3.5 14.0 + - - -
72C LYS* 3.7 8.7 + - + +
75C LEU* 3.6 27.7 - - + +
114C CYS* 1.3 82.5 - - - +
116C LYS* 1.3 59.7 + - - +
117C LEU* 3.1 29.2 + - + +
124C LYS* 3.8 31.4 + - + -
125C SER* 4.3 6.3 - - - -
128C ASP* 3.2 31.3 + - - +
131C PRO* 5.2 3.5 - - - +
132C PHE* 5.7 0.7 - - - -
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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