Contacts of the strand formed by residues 200 - 208 (chain B) in PDB entry 1F15
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 200 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B THR* 4.3 10.5 - - - +
75B LEU 4.0 5.6 - - - +
76B LYS* 3.9 35.0 - - + +
77B PRO* 4.8 0.2 - - - -
112B ASN 3.2 18.4 + - - +
114B LEU* 4.5 10.8 - - + -
197B ASP* 6.0 0.7 - - - +
199B LEU* 1.3 80.4 - - - +
201B LEU* 1.3 64.6 + - - +
202B HIS* 3.2 32.0 + - + +
144C ALA* 3.6 31.6 - - + +
145C ASP* 5.9 0.9 - - - -
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Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR* 3.6 0.3 - - - -
75B LEU* 3.0 50.2 + - + +
77B PRO* 3.7 23.3 - - + -
86B TYR* 4.2 2.9 - - + -
109B ILE* 4.9 10.1 - - + -
110B ARG 3.2 8.7 - - - +
111B VAL* 3.8 20.2 - - + -
123B VAL* 5.2 1.1 - - + -
185B VAL* 4.2 8.7 - - + -
187B VAL* 3.6 31.2 - - + -
199B LEU* 3.6 30.1 - - + -
200B VAL* 1.3 76.3 - - - +
202B HIS* 1.3 65.2 + - - +
203B VAL* 5.7 1.8 - - + -
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Residues in contact with HIS 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B SER* 5.5 3.1 - - - -
73B ILE 3.4 8.3 - - - +
74B THR* 3.9 21.7 - - + +
108B GLN 3.7 1.0 - - - +
109B ILE* 3.5 4.2 - - - +
110B ARG* 3.0 69.1 + - + +
112B ASN* 3.4 14.2 + - - -
200B VAL* 3.2 25.5 + - + +
201B LEU* 1.3 78.4 - - - +
203B VAL* 1.3 63.9 + - - +
204B ASP* 3.8 3.1 + - - +
144C ALA 3.1 27.8 + - - -
145C ASP* 3.6 18.0 + - - -
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR 3.8 0.3 - - - +
72B SER* 3.2 1.7 - - - -
73B ILE* 2.7 46.3 + - + +
75B LEU* 4.3 17.5 - - + -
90B LEU* 3.5 36.1 - - + -
107B LEU* 4.8 4.0 - - + -
108B GLN 3.5 4.7 - - - +
109B ILE* 4.1 14.1 - - + -
185B VAL* 3.9 24.7 - - + -
201B LEU* 5.5 1.6 - - + -
202B HIS* 1.3 76.8 - - - +
204B ASP* 1.3 62.9 + - - +
205B ILE* 3.7 13.9 + - + -
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Residues in contact with ASP 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A LEU* 5.2 3.5 - - + +
217A PRO* 3.1 12.1 - - + +
70B PHE* 4.1 14.1 - - + +
71B THR 3.6 3.6 - - - -
72B SER* 3.1 21.0 + - - +
106B ARG 4.0 0.5 - - - +
107B LEU* 3.7 0.3 - - - -
108B GLN* 2.7 66.4 + - + +
110B ARG* 2.9 30.9 + - - -
202B HIS* 3.8 4.9 - - - +
203B VAL* 1.3 75.2 - - - +
205B ILE* 1.3 62.1 + - - +
206B GLU* 3.5 4.2 + - - +
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Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B PHE* 3.1 3.6 - - - -
71B THR 2.7 33.5 + - - +
73B ILE* 3.8 15.7 - - + -
90B LEU* 4.3 12.3 - - + -
92B LEU* 3.4 39.9 - - + -
104B VAL* 4.0 30.3 - - + -
106B ARG 4.1 3.4 - - - -
107B LEU* 4.4 10.1 - - + +
177B ILE* 5.7 0.2 - - + -
180B MET* 4.4 11.7 - - + -
203B VAL* 4.2 16.4 - - + +
204B ASP* 1.3 71.0 - - - +
206B GLU* 1.3 62.5 + - - +
207B HIS* 3.5 13.7 + - - +
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A LEU* 4.3 16.9 - - + +
64B CYS* 3.2 13.1 - - + +
65B ARG* 2.9 30.9 + - - -
68B TYR* 3.8 9.9 - - + -
69B THR 3.2 13.9 - - - +
70B PHE* 3.7 3.3 - - - +
104B VAL* 3.4 9.5 - - - +
105B SER* 2.5 43.9 + - - +
106B ARG* 2.9 52.8 + - - +
204B ASP 3.5 3.4 + - - +
205B ILE* 1.3 71.5 - - - +
207B HIS* 1.3 59.8 + - - +
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Residues in contact with HIS 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B TYR* 3.2 12.5 - - - +
69B THR* 2.7 44.2 + - - +
70B PHE 4.4 1.1 - - - -
71B THR* 3.0 38.5 + - - -
92B LEU* 5.0 0.2 - - - +
96B VAL* 4.1 6.7 - - + +
102B LYS* 5.1 0.2 - - + -
103B LEU 2.9 18.2 - - - +
104B VAL* 4.1 6.3 - - + -
177B ILE* 3.4 32.6 - - + +
205B ILE* 3.6 16.9 + - + +
206B GLU* 1.3 74.4 - - - +
208B GLN* 1.3 91.9 + - - +
210B ILE* 4.1 13.2 - - + +
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Residues in contact with GLN 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B GLY 4.0 7.2 - - - +
68B TYR* 3.6 25.0 + - + -
101B LYS 4.4 0.9 - - - +
102B LYS* 3.5 27.2 - - + +
103B LEU* 2.6 63.0 + - - +
207B HIS* 1.3 100.1 - - - +
209B ARG* 1.3 69.6 + - - +
210B ILE* 3.6 0.5 + - - +
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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