Contacts of the strand formed by residues 127 - 138 (chain B) in PDB entry 4STD
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 ALA 127 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU 4.4 0.4 - - - -
107B ARG* 3.2 7.4 - - - +
108B VAL* 2.9 30.7 + - + +
125B GLY 3.9 2.2 + - - -
126B HIS* 1.3 73.4 - - - +
128B HIS* 1.3 60.7 + - - +
129B SER* 4.1 0.4 - - - -
151B ILE* 3.8 19.1 - - + -
153B TRP 3.8 5.2 - - - -
154B GLY* 4.4 2.5 - - - -
158B PHE* 3.9 12.3 - - + -
174B BFS 3.0 36.1 - - + -
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Residues in contact with HIS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU 3.6 5.2 - - - -
107B ARG* 4.0 16.3 + - + +
126B HIS* 3.1 24.0 + - + -
127B ALA* 1.3 70.5 - - - +
129B SER* 1.3 59.8 + - - +
151B ILE* 3.8 0.6 - - - -
152B ARG* 2.9 28.4 + - + +
153B TRP* 3.0 74.6 + + - +
155B GLU* 3.7 13.8 + - + +
84C GLN* 3.2 33.7 - - + +
109C PRO* 3.8 15.0 - - + +
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLN* 3.7 3.8 - - - +
106B LEU* 2.9 35.2 + - - +
127B ALA 4.1 0.4 - - - -
128B HIS* 1.3 76.5 - - - +
130B ALA* 1.3 57.0 + - - +
131B ASN* 2.8 25.7 + - - -
150B ASP 2.9 22.0 - - - -
151B ILE* 3.6 17.7 - - - -
152B ARG* 4.2 5.4 - - - +
174B BFS 3.4 16.6 - - - -
84C GLN* 4.0 3.5 + - - +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR* 6.4 1.1 - - + -
104B HIS 3.8 4.7 - - - -
105B GLN* 4.9 1.1 - - + +
129B SER* 1.3 73.0 - - - +
131B ASN* 1.3 64.3 + - - +
132B LEU* 3.9 0.5 + - - +
148B LYS 3.7 2.9 - - - +
150B ASP* 3.0 28.9 + - + +
152B ARG* 3.6 36.1 - - - +
24C TYR* 4.0 17.3 - - - +
28C ASP* 4.1 4.5 - - - +
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Residues in contact with ASN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TRP* 4.2 0.5 - - - -
102B GLY 3.5 1.0 - - - +
103B TYR* 3.3 7.5 - - - +
104B HIS* 2.8 44.4 + - + +
106B LEU* 3.9 16.3 - - + +
129B SER* 2.8 29.3 + - - -
130B ALA* 1.3 73.0 - - - +
132B LEU* 1.3 59.8 + - - +
133B HIS* 3.2 28.2 + - + +
147B LEU* 3.9 1.0 - - - +
148B LYS 3.9 2.0 - - - -
149B PRO* 3.5 25.9 - - - +
174B BFS 2.9 25.1 + - - -
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Residues in contact with LEU 132 (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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101B ILE* 3.8 22.9 - - + -
102B GLY 3.5 3.6 - - - -
103B TYR* 3.7 33.7 - - + +
130B ALA 3.9 0.9 + - - +
131B ASN* 1.3 73.2 - - - +
133B HIS* 1.3 62.6 + - - +
134B TRP* 3.3 44.4 - - + +
147B LEU* 3.2 2.8 - - - -
148B LYS* 2.6 75.7 + - + +
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Residues in contact with HIS 133 (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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23B VAL* 4.1 1.9 - - + +
26B TRP* 3.5 37.5 - + - -
101B ILE* 3.3 9.5 - - - +
102B GLY 2.8 29.2 + - - +
104B HIS* 3.4 17.9 - + - +
106B LEU* 5.1 0.4 - - + -
131B ASN* 3.2 34.8 + - + +
132B LEU* 1.3 83.3 - - - +
134B TRP* 1.3 62.3 + - - +
135B TYR* 3.0 35.7 + - + +
144B PHE* 3.4 18.6 - + + -
146B GLY 3.5 5.2 - - - +
147B LEU* 3.6 10.8 - - + +
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Residues in contact with TRP 134 (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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47B ARG* 3.4 57.0 - - + -
49B ASP* 4.1 7.4 - - + -
95B VAL* 6.0 0.4 - - + -
100B VAL 3.6 3.4 - - - +
101B ILE* 3.9 26.6 - - + +
132B LEU* 3.3 23.4 - - + +
133B HIS* 1.3 72.6 - - - +
135B TYR* 1.3 64.9 + - - +
136B LYS* 6.2 0.2 - - + -
144B PHE* 4.1 0.7 - - - -
145B ALA* 2.8 36.4 + - + +
146B GLY* 2.9 29.9 + - - +
147B LEU* 3.4 17.9 - - - -
148B LYS* 3.5 27.6 - - + -
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Residues in contact with TYR 135 (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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19B LEU* 3.7 22.7 - - + -
22B CYS* 3.9 24.2 - - + -
23B VAL* 3.5 12.6 - - + +
92B TRP* 3.1 36.6 - + - -
99B GLU* 3.4 7.1 - - - +
100B VAL* 2.7 43.4 + - + +
102B GLY 3.9 7.0 - - - -
104B HIS* 2.6 26.7 + - - -
133B HIS* 3.0 30.0 + - + -
134B TRP* 1.3 76.3 - - - +
136B LYS* 1.3 63.6 + - - +
142B TRP* 3.6 6.9 - - + -
143B LYS 3.1 15.3 - - - +
144B PHE* 3.9 19.1 - + - -
145B ALA 4.2 0.2 - - - +
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Residues in contact with LYS 136 (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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43B ALA* 4.8 4.7 - - + -
45B THR 6.0 0.2 - - - +
98B ASP* 2.9 27.8 + - - +
99B GLU* 4.0 29.4 + - + +
134B TRP* 6.2 0.2 - - + -
135B TYR* 1.3 73.4 - - - +
137B LYS* 1.3 58.6 + - - +
138B ILE* 3.2 27.6 + - + -
142B TRP* 3.7 3.6 - - - -
143B LYS* 2.7 40.4 + - - +
145B ALA* 3.4 25.4 - - + -
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Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASP* 4.1 14.2 + - - +
97B GLU 4.2 13.2 - - - +
98B ASP* 2.8 36.4 + - + +
136B LYS* 1.3 68.7 - - - +
138B ILE* 1.3 61.5 + - - +
139B ASP 4.0 1.2 + - - -
140B GLY* 3.5 33.5 + - - +
141B VAL 3.4 11.4 - - - +
142B TRP* 3.6 39.6 - - + +
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Residues in contact with ILE 138 (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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43B ALA* 3.9 15.0 - - + -
44B PRO* 3.6 32.3 - - + -
136B LYS* 3.2 24.2 + - + +
137B LYS* 1.3 74.8 - - - +
139B ASP* 1.3 84.1 + - - +
141B VAL* 2.7 26.8 + - - +
143B LYS* 4.1 20.8 - - + -
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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